Regional Studies in Marine Science 43 (2021) 101674

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Regional Studies in Marine Science

journal homepage: www.elsevier.com/locate/rsma

Hydrodynamic modeling of salinity habitat changes with reduced

submarine groundwater discharges in a spring-fed estuary
XinJian Chen 1
Natural Systems and Restoration Bureau, Southwest Florida Water Management District, 7601 Highway 301 North Tampa, FL 33637, USA

article info a b s t r a c t

Article history: Effects of reduced submarine groundwater discharge (SGD) on salinity habitats were studied for a
Received 15 December 2020 narrow spring-fed estuary. A laterally averaged model was used to simulate circulations, salinity
Received in revised form 10 February 2021 transport processes, and thermal dynamics in the estuary. It was calibrated and verified against
Accepted 11 February 2021
measured water elevations, salinities, and temperatures at five stations during November 2014–August
Available online 16 February 2021
2017, before it was used to evaluate effects of SGDs on salinity habitats during a 125-month period.
Keywords: Salinity habitats considered and analyzed here included water volumes, bottom areas, and shoreline
SGD lengths for salinity ≤ 1, 2, 3, 5, 10, and 15 psu.
Spring-fed estuary It is found that the long-term (hourly) and short-term (monthly or longer) responses of salinity
Coastal springs habitats to the SGD reduction are different in the estuary. Long-term average salinity habitats have a
Hydrodynamic simulations linear relationship with the SGD reduction. Except those for salinity ≤ 1 psu, long-term oligohaline
Laterally averaged hydrodynamic model salinity habitats in the estuary are more sensitive to the SGD than salinity habitats with mesohaline
Salinity habitats
salinity zones being included. Long-term average water volumes and bottom areas of ≤2 psu are most
sensitive to the SGD and they can be reduced by 1.38% for every 1% of SGD reduction. The short-term
response of salinity habitats is greatly affected by special physical features in the estuary, and the
sensitivity of a salinity habitat to the SGD varies with the location of the isohaline in relationship with
these physical features. For example, when the 2 and 3 psu isohalines pass a narrow transect in the
upstream area of the estuary, ≤2 and 3 psu salinity habitats become much more sensitive to the SGD
than other locations of the isohalines. On the other hand, when the 5 and 10 psu isohalines enter the
downstream distributaries, ≤5 and 10 psu salinity habitats are most sensitive to the SGD.
Published by Elsevier B.V.

1. Introduction wetland is self-percolating and barely contributes any quantifi-

The Homosassa River is a small spring-fed estuary located on
the Gulf coast of central Florida (Fig. 1). From its headspring to
the Gulf of Mexico (GOM), the estuary is about 13 km long and
has a width varying from about 60 m in the upstream reach to
about 305 m near the mouth (Yobbi and Knochenmus, 1989).
Except for the navigation channel and some deep holes, most
of the riverbed is less than 1 meter deep under the mean tide
level. The estuarine system includes several tributaries, among
which the SE Folk and the Hall River enter to the upstream area
of the Homosassa River, while the Salt River and Mason Creek are
connected to the downstream part of the estuary. The river also
has some other smaller tributaries, including a channel system in
the town of Homosassa and the Hidden river.
The Homosassa River flows through a coastal swamp region,
where poorly drained and saturated organic soils overlie lime-
stone rocks of the Upper Florida Aquifer (UFA). As most of the
E-mail address: xinjian.chen@swfwmd.state.fl.us.
1 Chief Professional Engineer, Southwest Florida Water Management District.
able surface water runoff, the estuary receives an insignificant
amount of freshwater runoff from its 145 km2 Watershed. Most
of the hydrologic loading to the Homosassa River comes from
the UFA in the form of submarine groundwater discharges (SGDs)
out of numerous spring vents located in the headspring area and
several tributaries, including the SE Fork and the Halls River. The
Homosassa River has a springshed of about 700 km2 , with a slight
year-to-year variation as the contributing groundwater field for
the spring discharge is subject to the shape of potentiometric
contours in the region. Locations of the springs that discharge
groundwater flows to the Homosassa River are shown as solid
dots in Fig. 1. The headwaters of the river are the Homosassa
Springs, and several other springs. Because nearly all flows en-
tering the Homosassa River estuary are SGDs, SGD and flow are
exchangeable in this article.
On each side of the Homosassa River, there is an extensive
wetland system. As plant species are sensitive to changes in salin-
ity, different plants are distributed in the wetland and along the
shoreline of the estuary. Salinity in the Homosassa River estuarine
system exhibits a natural gradient from the headsprings to the

https://doi.org/10.1016/j.rsma.2021.101674
2352-4855/Published by Elsevier B.V.
X. Chen
Fig. 1. Aerial view of the Homosassa River on the Gulf coast of Florida. Triangles mark locations of USGS real-time data stations along the river.
GOM. As a result, hydric hammocks can be found near the freshest
waters in the upstream areas, especially along the southeast fork
of the Homosassa River, while salt marshes and coastal hydric
hammocks are found in the downstream areas where salinity is
high (Leeper et al., 2012).
The mouth of the Homosassa River is located near the center of
the southern half of the Florida Big Bend Coast, which is roughly
from the mouth of the Suwannee River, located about 21 km
northwest of Cedar Key, Florida, to the mouth of the Anclote River
near Tarpon Springs, Florida. Macroscopically, the coastline of this
part of the Florida Big Bend Coast looks like an arc of a circle.
The circular segment has a sagitta of about 32 km and a chord
length of about 130 km. The central angle and the area of the
circular segment can be estimated to be about 105 degrees and
2,900 km2 , respectively. Several rivers drain a large amount of
freshwater flows to this relatively shallow coastal water, where
most areas are less than 2 m deep. These rivers include the
Suwannee River, Withlacoochee River, and four major spring-
fed estuaries (Crystal, Homosassa, Chassahowitzka, and Weeki
Watchee Rivers). The Suwannee River alone drains a watershed of
approximately 25,770 square kilometers stretching from northern
Florida to southern Georgia, and the Withlacoochee River has a
watershed of about 5,440 square kilometers. Each of the four
spring-fed estuaries receives SGDs from first magnitude springs
or spring groups.
Because of the relatively large amount of hydrologic loading
received, salinity along the Florida Big Bend Coast is generally
low. At the mouth of the Homosassa River, recorded salinity
generally varies between < 15 psu to < 25 psu most of the time of
the year. Only during the end of the dry season, which generally
starts in late April and ends in late June for the region, will salinity
at the river mouth reach 30 psu or more at high tides. Like some
other estuaries along the Gulf coast of Florida, the Homosassa
River estuary is under the action of microtidal forces, which
are primary diurnal and semidiurnal. As the estuary is relatively
shallow, the Homosassa River is generally well or partially mixed.
There are only limited previous studies on effect of SGDs
on salinity habitats in the Homosassa River estuary. Yobbi and
2
Regional Studies in Marine Science 43 (2021) 101674
Knochenmus (1989) tried to find relationships among salinities,
tides, and SGDs in the Homosassa River by examining measured
data at fixed gage stations during 1984 and 1985 with some
sporadic data collected at several additional sites. They found that
the water column was typically well-mixed, with the top-layer
salinity being generally less than 15% lower than the bottom-layer
salinity. During the two-year period, salinity at the downstream
side of the confluence of the Homosassa and Halls Rivers typically
fluctuated between one to two psu when the river mouth had a
salinity ranging approximately 13–26 psu. Yobbi and Knochen-
mus (1989) noticed that the 2 psu isohaline varied over a 2.8-km
stretch between river km 7.2 to river km 10.0. On the other hand,
the 25 psu isohaline varied over a stretch of 8.6 km, between
river km -8 to river km 0.6. Although these observations represent
actual salinity variations in the estuary, Yobbi and Knochenmus
(1989) did not give a physically reasonable explanation for what
they observed. HSW Engineering (2011) applied the Environmen-
tal Fluid Dynamics Code (EFDC), originally developed by Hamrick
(1992), to simulate circulations and salinity transport processes
in the Homosassa River. They had to expand and deepen the
downstream area of the river to form a large funnel to allow
salt water to be transported upstream in their EFDC application
(HSW Engineering, 2011). Clearly, this artificial alteration of the
topography and bathymetry dramatically changed the shape of
the estuary that was simulated and should not be made in any of
hydrodynamic modeling studies. Model results from an estuary
that has a dramatically different shape from the real estuary are
meaningless.
Because the Homosassa River is a narrow and meandering es-
tuary, its circulation pattern and salinity and temperature distri-
butions vary primarily in the vertical and longitudinal directions.
Vertically two-dimensional variations are typical for narrow es-
tuaries (Prandle, 1985; Jay and Smith, 1990; Chen, 2003), for
which the most suitable simulation tool is a laterally averaged
model. This study used the Laterally Averaged Model for Estu-
aries (LAMFE), developed by the author, for the simulation of
circulations, salinity transport processes, and thermal dynamics
X. Chen
in the Homosassa River. The LAMFE model has been applied to
several estuaries over the last two decades, including the lower
Hillsborough River (Chen and Flannery, 1997; Chen et al., 2000;
Chen, 2004a), the lower Alafia River (Chen, 2004b; Flannery et al.,
2007), the lower Peace and Myakka Rivers (Chen, 2007, 2008,
2010), and the lower Manatee/Braden Rivers (Chen, 2012a).
As mentioned in Chen (2014), most previous coastal and es-
tuarine hydrodynamic modeling studies did not consider effects
of SGDs (Johnson et al., 1991; Blumberg and Kim, 2000), partly
because SGDs are much lower than river flows and precipitations
for these estuaries and partly because SGDs are very difficult to
quantify in many cases. There are only very limited estuarine
and coastal hydrodynamic modeling studies which considered
SGDs. Ganju et al. (2012) applied the 3D model ROMS (Warner
et al., 2008) to West Falmouth Harbor, Massachusetts to verify
their tidal and groundwater flux estimates to the estuary based
on velocity and salinity measurements. Chen (2014) estimated
and considered SGDs in the hydrodynamic simulations for Crystal
River/Kings Bay in using the 3D model UnLESS3D to analyze
thermal habitats for manatees in the spring-fed estuary. It was
found that SGDs in Crystal River/Kings is not only negatively
proportional to the tides but also positively proportional to the
first derivative of tides with respect to time.
In the following sections, available data in the spring-fed es-
tuary are described, with major physical characteristics being
discussed. The LAMFE model application to the Homosassa River
is then presented with a brief description of model setup and
model calibration and verification. Effects of SGD on salinity habi-
tats in the Homosassa River estuary are analyzed after a series of
model runs were conducted. Conclusions of the modeling study
are provided at the end of the paper.
2. Measured and estimated data
Different types of reliable data are needed for a successful
simulation of estuarine and coastal hydrodynamics. These data
include topographic and bathymetric data, flow data, meteoro-
logical data, and real-time data of water elevation, salinity, and
temperature. While topographic and bathymetric data are to
define the shape of the estuary, meteorological data and some
other data are to drive the hydrodynamic model. For model
calibration and verification, real-time water levels, salinities, and
temperatures recorded at stations inside the simulation domain
will be needed to ensure that the numerical model performs well
for the waterbody.
2.1. Topographic and bathymetric data
For the Homosassa River estuary, bathymetric data were col-
lected by surveying cross sections along the main stem of the
river and its tributaries. Topographic data collected using the
Light Detection and Ranging (LiDAR) technique are available for
the region. These data show that the Homosassa River estuary is
generally shallow, with the water depth being less than one me-
ter most of the area. The upstream segment of the main stem and
the tributaries are shallower than the middle and downstream
segment of the Homosassa River. The elevation of the thalweg of
the Homosassa River main stem varies from about −1.0 m NAVD
88 in the upstream area to about −6.6 m, NAVD88 in the middle
segment of the river.
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Regional Studies in Marine Science 43 (2021) 101674
2.2. Water level, salinity, and temperature data
There were several fixed stations in the Homosassa River
system, at which real-time data were collected for water eleva-
tion, salinity, and temperature with a time interval of 15 min.
Most of these stations were maintained by the United States
Geological Survey (USGS). Yellow triangles in Fig. 1 show loca-
tions of the USGS real-time stations, including (1) Homosassa
River at Shell Island near Homosassa (#02310712), (2) Homosassa
River at Homosassa (#02310700), (3) Halls River near Homosassa
(#02310690), (4) Halls River at Homosassa Springs (#02310689),
(5) Homosassa Springs at Homosassa Springs (#02310678), (6)
SE Fork Homosassa Spring at Homosassa Springs (#02310688),
and (7) Hidden River near Homosassa (#02310675). More de-
tails about these USGS real-time stations can be found in Chen
(2019a). In addition to the USGS stations, two additional fixed
stations by the Southwest Florida Water Management District
(SWFWMD) were available for the Salt River and Mason Creek
(see red triangles marks in Fig. 1 for their locations.)
Measured real-time data of water level, salinity, and tempera-
ture indicate that the Homosassa River estuary is a low energy
system. Although tidal signals are recorded everywhere in the
river, they generally have a tidal range of less than 30 cm. Even
at the station near the mouth of the estuary, tides generally
vary within a range of 50 cm or less. Tides in the estuary are
primarily diurnal and semidiurnal; however, non-tidal and low
frequency signals also exist in measured real-time water levels at
all stations. These low frequency variations are mainly influenced
by meteorological and hydrological characteristics of the region.
Because of the physical setting of the estuarine system, tides
are attenuated quickly as they propagate from the mouth to the
upstream segment of the Homosassa River. From the Homosassa
River at Shell Island station near the mouth to the Homosassa
River at Homosassa station, about two thirds into the estuary,
tides lose about one half of their variabilities. In other word,
about 75% of tidal energy is lost along two thirds of the river. In
the tidal reach upstream of the Homosassa River at Homosassa
station, up to the headwaters of the river, the tidal energy atten-
uation becomes small, as tidal waves attenuate only slightly while
propagating further upstream.
One of the reasons for this phenomenon of different tidal
energy losses is that the downstream reach is almost two times
of the length of the upstream reach, causing the tidal energy
to lose more in the downstream reach than in the upstream
reach. Another reason is that the tidal currents in the downstream
part are stronger than these in the upstream part of the estuary.
Nevertheless, a major reason for the large tidal energy loss in the
downstream reach may be caused by a few narrow segments in
the downstream portion of the river, especially the one at around
the half way between the Homosassa River at Shell Island and
Homosassa River at Homosassa stations, which is about 2 km long
and greatly restricts the passage of tidal energy passing through
it.
Salinity and temperature variabilities in the downstream area
of the Homosassa River are dominated by processes in the GOM,
while in the upstream area, they are dominated by SGDs. Al-
though measured salinities and temperature at upstream stations
contain tidal signals, their variabilities are weak. For example, at
the Homosassa Springs at Homosassa Springs station, measured
temperature was almost constant at about 23 ◦ C, with a very
insignificant daily and seasonal variations. During winter, water
temperature at the mouth can drop to 10 ◦ C or lower but the
upstream area near Homosassa Springs and the SE Fork were
warm with temperature higher than 20 ◦ C during these cold days.
Further downstream in the Homosassa River and in Halls River,
the low water temperature was about 15 ◦ C, which was still
X. Chen
roughly 5 ◦ C higher that at the river mouth, because of the warm
SGDs flowing to the estuarine system.
At the cross section of the SE Folk station, flow is mostly
fresh (< 0.5 psu) and only occasionally a salinity peak of only
1–1.5 psu would occur. The SE Fork Homosassa Spring station is
about 130 meters to the confluence with the Homosassa River,
which is roughly the same distance to the Homosassa Springs
at Homosassa Springs. While salinity at the SE Fork station is
barely higher than 1 psu, salinity measured at the Homosassa
Spring at Homosassa Springs is barely less 1 psu. This suggests
that SGDs from SE Fork springs, including Belcher Spring, Trotter
Springs, McClain Spring, and Pumphouse Spring are fresh and
the occasional salinity peaks are caused by high tides. Under
the normal condition, the freshwater–salt water interface moves
back and forth around the SE Fork station, with its location being
downstream of the station most of the time. As salinity at the SE
Fork station comes from the estuarine part of the river, not from
the SGD, it can be concluded that SGD gaged at the SE Fork is
fresh. It is not expected that a reduction of SGD would cause any
salinity increases in SGD (Chen, 2019b).
Although the Halls River at Homosassa Springs station is lo-
cated upstream of the Halls River near Homosassa station, salinity
measured at the upstream station is about 2 psu higher than that
measured at the downstream station. Obviously, SGD entering
the upstream of the Halls River is brackish. The relatively flat
salinity peaks suggest that the upstream SGD is a salinity source
for the Halls River and salinity in the SGD is quite stable under
various discharge conditions. The relatively lower salinity at the
downstream station is caused by the fresher SGDs from SE Fork
and Homosassa headwaters, because the Halls River near Ho-
mosassa station is close to the confluence of the Halls River with
the Homosassa River. The tidal currents transport fresher water
upstream to dilute the brackish SGD in the upstream portion of
the Halls River. The moderately flat salinity peaks generally varied
at around 5 psu and it is possible that salinity in the upstream
SGD of the Halls River is the same or slightly higher than that
measured at the Halls River at Homosassa Springs station.
One thing that can be noticed from the measured salinity
data is that salinity at the Homosassa River at Homosassa station
does not correlate well with salinity at the river mouth. Several
salinity signals that are strong at the mouth are nonexistent or
become weak at the Homosassa River at Homosassa station, and
vice versa. A regression between salinities at the two stations has
a R2 of less than 0.5, even when various time leads/lags were
considered, suggesting that salinity in the upstream half of the
estuaries are more dominated by SGDs and/or factors other than
those occurring in the GOM.
2.3. Flow data
As mentioned above, most of the hydrologic loading to the
Homosassa River estuary comes from the various spring vents and
the quantification of the SGD is very difficult because of the com-
plexity of spring vents and the impact of tides on the discharge
rate. Some of the limestone vents are clustered together and
connected. There could be interactions among these spring vents.
It is generally infeasible to measure the discharge from each
individual spring vent. As a result, the combined SGD from several
spring vents is generally measured at a proper downstream cross
section of these vents. The USGS has been deploying acoustic
Doppler current Profilers (ADCPs) to the estuary and using the
index velocity method to calculate SGDs entering the SE Folk
and the Halls River since October 1, 2011 and March 10, 2012,
respectively. The USGS also has an ADCP at the Homosassa River
at Homosassa station to record the combined SGD upstream of
the cross section since October 1, 2006. SGD gaged at this station
4
Regional Studies in Marine Science 43 (2021) 101674
comprises most of the hydrologic loading to the estuary. The only
SGD missing from this station is that entering the Hidden River
(Fig. 1), which is gaged at the USGS Hidden River near Homosassa
station.
Although Homosassa Springs are the headwater for the estu-
ary, the USGS does not have an ADCP deployed downstream of
these spring vents to record SGDs due to the lack of a proper cross
section downstream of the vents. Based on limited discharge data,
a regression equation was obtained by the USGS that relates
the discharge of Homosassa Springs with the water level at the
site and the groundwater level in a well in Weeki Wachee. This
regression equation was updated several times over the years.
The most recent version, valid since October 1, 2013, takes the
following form
Qhs = 76.863 − 20.7636h + 5.3139W (1)
where Qhs (in cfs) is the flow rate for Homosassa Springs at
Homosassa Springs, h is water level (feet, NGVD29) and W is
Weeki Wachee well level (feet, NGVD29).
For the SE Fork discharge before October 1, 2011, the USGS
also has a regression equation as follows
Qse = 18.6293 − 10.3114h − 418.139∆h + 3.31029W (2)
where Qse (in cfs) is the flow rate through the SE Fork Homosassa
station and ∆h is the water level change over the data collection
interval (15 min).
Both Equations (1) and (2) show that the SGD is positively
proportional to the groundwater level but negatively proportional
to the water elevation in the Homosassa River. However, Eq. (2)
has an extra term suggesting that SGDs from spring vents up-
stream of the SE Folk station is also linearly related to the water
level change over the 15-minute interval of data collection. This
is consistent with a previous study on effects of tides on SGD in
Crystal River/Kings Bay (Chen, 2012b, 2014). Chen (2014) found
that the time derivative term is necessary not only to properly
match the phase in the tidal signal of the measured SGD but also
to model the high frequency variabilities observed in the SGD
data.
Fig. 2 shows discharge data at all the stations in the Homosassa
River system. For clarity, only 2016 was shown in the figure
and discussed here. Discharge data collected/estimated for other
years can be found in Chen (2019a). As can be seen from Fig. 2,
most discharge data contain significant tidal signals, mainly due
to the existence of tidal prisms upstream of these stations. The
Homosassa River at Homosassa has the biggest upstream tidal
prism, resulting in the biggest tidal flux varying between about
-1,000 cfs to about 1,000 cfs. The Hidden River discharge has only
insignificant tidal signals but has a clear seasonal variability.
The big positive/negative peaks shown in Fig. 2 were during
days of Hurricane Hermine in 2016. Hermine developed in the
Florida Straits on August 28, 2016 and made landfall in the Florida
Panhandle on September 2, 2016. As presented in Chen (2019a),
during these hurricane days, the SE Fork Homosassa Spring sta-
tion had a negative discharge peak of more than 400 cfs, while the
Homosassa River at Homosassa station had a negative discharge
peak of almost 10, 000 cfs.
An analysis of measured SGDs was conducted for all the sta-
tions and it was found that the long-term average of SGD gaged
at the Homosassa River at Homosassa station is roughly equal to
the sum of those gaged at the SE Fork Homosassa Spring station,
the Homosassa Springs at Homosassa Springs station, and the
Halls River at Homosassa Springs station. In other words, there
is no noticeable ungaged flow upstream of the Homosassa River
at Homosassa station. For example, during September 30, 2016–
March 13, 2018, average SGDs were 177.09 cfs, 56.77 cfs, 90.90
cfs, and 30.58 cfs at the Homosassa River at Homosassa, SE Fork
X. Chen
Fig. 2. Measured and estimated discharge data in the Homosassa River system during 2016.
Homosassa Spring, Homosassa Springs at Homosassa Springs, and
Halls River at Homosassa Springs stations, respectively. The three
upstream stations had a total of 178.25 cfs, which was very close
to the average discharge of 177.09 cfs at the Homosassa River at
Homosassa station.
2.4. Meteorological data
Meteorological data that are available for study included wind
speed, wind direction, air temperature, air humidity, and solar
radiation at a SWFWMD weather station near Inglis, Florida and
at a Florida Automated Weather Network (FAWN) station by the
University of Florida’s Institute of Food and Agricultural Science
(UF/IFAS). The former is about 16 miles north of the Homosassa
River, while the latter is about 6 miles northeast of the river. The
region has distinct winter and summer patterns. In the winter,
frequent frontal incursions and extratropical cyclones can pro-
duce large shifts in wind speed and wind direction in response to
rapidly changing atmospheric pressure and thermal gradients. In
the summer, the weather is generally characterized by light and
variable winds originating from the northeast trade wind circu-
lation. Sea/land breezes are typical due to the strong differential
heating of the land and adjacent waters along the coast during
the summer months. Occasional tropical storms can move to the
area during summer, causing a temporal but sometimes intense
modification to the meteorological conditions of the region.
3. Model calibration and verification
3.1. Model setup
For the LAMFE model application, the Homosassa River estu-
ary, was discretized with 406 grids along the river main stem and
its 21 branches to ensure that the main physical of the system
can be properly resolved by the model. The horizontal spacing of
5
Regional Studies in Marine Science 43 (2021) 101674
the grids varies between 29 to 277 m. Fig. 3 shows cross sections
that form the 406 LAMFE grids along the estuarine system. In the
vertical direction, 15 layers, varying from 0.3 to 1.76 m, were used
to discretize the water depth ranging between −6.56 m, NAVD88
to 3.0 m, NAVD88.
Based on the availability of measured data which were used
to drive the model, a 34-month period between 11/4/2014 and
8/31/2017 was chosen for model calibration and verification.
During this 34-month period, SGDs and meteorological data were
available. Water elevation, salinity, and temperature data at the
mouth of the Homosassa River were also available. However,
there were no water elevation, salinity, and temperature data
for the open boundaries in the Salt River and the Mason Creek
for the entire 34 months, except for a 4-month period in 2017.
To obtain boundary conditions of water elevation, salinity, and
temperature in the Salt River and Mason Creek for the entire
34 months, an effort was made to correlate water elevations,
salinities, and temperatures measured at the Salt River and Mason
Creek stations with those at other data collection stations with
longer period of record. It was found that water level, salinity,
and temperature data in the Salt River and Mason Creek are best
correlated with those measured at the mouth of the Homosassa
River. A trial and error approach with various time lags or leads
was used to obtain the best correlations. Details about estimating
boundary conditions of water level, salinity, and temperature in
the Salt River and Mason Creek are documented in Chen (2019a).
As discharges from spring vents are measured at proper tran-
sects downstream of these groundwater sources, measured flow
data contain tidal fluxes through these transects. To obtain net
SGDs entering the upstream reaches of the cross sections, tidal
fluxes were estimated through the following formula and taken
away from the reported discharge data.
∂η
qt = −A (3)
∂t
X. Chen
Fig. 3. Cross sections (yellow segments) that form the LAMFE grids for the Homosassa River and its branches. Numbers in green are grid numbers in the longitudinal
direction. Orange arrows are locations where SGDs enter the model domain. (For interpretation of the references to colour in this figure legend, the reader is referred
to the web version of this article.)
where qt is the tidal flow, with the positive flow pointing toward
downstream, η is measured water level, t is time, and A is the
surface water area upstream of the cross section.
Except for the Hidden River, net SGDs were added to the
model domain at the most upstream grids of the main stem and
branches of the estuarine system, instead of at the stations where
discharges were measured or estimated. Orange arrows in Fig. 3
indicate locations where SGDs enter the model domain.
Because no direct measurements of salinity and temperature
in the spring vents were available for this modeling study, salinity
and temperature in SGD was an unknown and needed to be
reasonably estimated. This study used a trial and error approach
to estimate salinities and temperatures in all the SGDs. Based on
measured salinities and temperatures at the SE Fork Homosassa
Spring station, the Homosassa Springs at Homosassa Springs sta-
tion, and the Halls River at Homosassa Springs station, many
salinity and temperature estimates were tested in model runs.
After a careful analysis of simulated salinity and temperature
results, it was found that it is suitable to use measured salinity at
the Homosassa Springs at Homosassa Spring for the Homosassa
Main SGD and measured salinity at the Halls River at Homosassa
Springs station for the Halls River SGD. For the SE Fork, the best
SGD salinity estimate takes the following form
Sse = max(0.952Ssef , 0.3)
where ssef represents measured salinity at the SE Fork Homosassa
Spring station and sse is the estimated salinity in SGD entering the
SE Fork. The best estimate for SGD temperature is a combination
of measured temperature and a constant value of 23.5 ◦ C. More
details about estimating salinity and temperature in SGDs are
reported in Chen (2019a).
3.2. Comparisons of model results with field data
The 34-month simulation period was divided into a model
calibration period and a model verification period. The former
was 11/4/2014–5/31/2016, while the latter was 6/1/2016–
8/31/2017. Model calibration involves a series of adjustment of
Regional Studies in Marine Science 43 (2021) 101674
model parameters within certain allowable ranges to obtain the
best match of simulated water levels, salinities, and temperatures
with measured data collected in the field. The LAMFE model for
the Homosassa River was mainly calibrated against measured
real-time data at the five USGS station: SE Fork Homosassa
Spring, Homosassa Springs at Homosassa Springs, Halls River at
Homosassa Spring, Halls River near Homosassa, and Homosassa
River at Homosassa stations. Only limited LAMFE model param-
eters had to be tuned in the calibration process, including the
bottom roughness, ambient vertical eddy viscosity and diffusivity,
and light attenuation. LAMFE allows different river segments to
be assigned with different values for these model parameters,
among which, ambient vertical eddy viscosity is the most sen-
sitive parameter for salinity simulation and light attenuation is
the most sensitive parameter for temperature simulation. The
model was best calibrated with an ambient vertical eddy viscosity
of 0.10 cm2 /s, a light attenuation coefficient of 0.004 1/cm, and
a bottom roughness height (z0 ) and an ambient vertical eddy
diffusivity in the ranges of 0.10–0.12 cm and 0.05–0.10 cm2 /s,
respectively.
Comparisons of model results with measured field data at
the five measurement stations in the Homosassa River estuarine
system are presented in Figs. 4–6. In these time series plots, red
lines are model results, while dashed green lines are measured
(4)
data. For simplicity and clarity, only 60 days of model results
and field data of water level, salinity, and temperature, between
1/5/2015 and 3/5/2015, are shown in Figs. 4–6. The choice of
these 60-day period is arbitrary. Comparisons of model results
with real-time field data during other time periods are similar,
with some having a slightly better match and some a slightly
worse match. Time series plots showing comparisons of model
results with field data of water level, salinity, and temperature
during other time periods are reported in Chen (2019a).
As can be seen from Fig. 4, simulated water elevations at all
five USGS stations agree very well with measured data. Simulated
water levels have the same long-term and short-term variations
as measured data. Modeled salinity and temperature results also
have good agreement with field data (Figs. 5 and 6), both in
6
X. Chen
Fig. 4. Comparison of measured and simulated water levels at the SE Fork Homosassa Spring, Homosassa Springs at Homosassa Spring, Halls River at Homosassa
Spring, Halls River near Homosassa, and Homosassa River at Homosassa stations during 1/5/2015 through 3/5/2015.
terms of long-term and short-term variations. Because of the
uncertainties included in the input data that drive salinity and
temperature simulations, it is expected that the match between
model results and data for salinity or temperature is not as good
as that for water level simulation. Nevertheless, simulated salin-
ity and temperature results are satisfactorily well matched with
measured data. The reversed salinity distribution in Halls River,
where upstream salinity is higher than downstream salinity, was
correctly simulated.
3.3. Model performance metrics
The performance of the LAMFE model for the Homosassa River
is accessed quantitatively with several statistics, including the
mean error (ME), mean absolute error (MAE), root-mean-square
error (RMSE), normalized root-mean-square error (NRMSE), co-
efficient of determination (R2 ), and a skill assessment param-
eter (Skill) introduced by Willmott (1981). The Willmott skill
assessment parameter takes the following form
∑ M
(y − yD )2
Sk = 1 − ∑ ⏐ ⏐ (5)
(⏐yM − yD ⏐ + |yD − yD |)2
⏐ ⏐
where Sk is the skill assessment parameter; yM and yD represent
simulated and measured variables; and yD is the expectation of
yD . Sk in the above equation varies between 0 and 1, with one be-
ing a perfect agreement and zero being a complete disagreement
between simulated results and measured data.
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Regional Studies in Marine Science 43 (2021) 101674
Table 1 summarizes MEs, MAEs, RMSEs, NRMSEs, R2 , and
Skills for simulated water elevations, salinities, and tempera-
tures. These statistics were calculated for the calibration period
(11/4/2014–5/31/2016) and the verification period (6/1/2016–
8/31/2017) separately. They were also calculated for the en-
tire simulation (calibration & verification) period (11/4/2014–
8/31/2017).
As can be seen from Table 1, the ME between simulated and
measured water elevations is about -1.53 cm during the calibra-
tion period, 0.79 cm during the verification period, and -0.64 cm
for the entire period. MAEs for the water elevation simulation
are 5.44, 5.68, and 5.54 cm for the calibration, verification, and
entire period, respectively. RMSEs are 7.17 cm, 7.29, and 7.21 cm,
for the calibration, verification, and the entire simulation periods,
respectively, with the corresponding NRMSEs being 0.04, 0.04,
and 0.03. The R2 values between simulated and measured water
levels are all 0.86 for the three periods, during which the Willmott
skills are all 0.96.
For salinity, MEs between model results and field real-time
data are −0.07, 0.14, and 0.0 psu, respectively during the calibra-
tion, verification, and entire periods, respectively. The MAEs are
about 0.39, 0.61, and 0.46 psu, respectively during the three peri-
ods, while RMSEs between simulated and measured salinities are
0.69, 1.01, and 0.81 psu, respectively. The NRMSEs for the salinity
prediction is 0.03, 0.04, and 0.03, respectively for the calibration,
verification, and entire periods. The R2 values between simulated
and measured salinity are 0.85, 0.81, 0.83, respectively for the
calibration, verification, and entire simulation periods, while the
Skills are 0.96, 0.95 and 0.95, respectively for the three periods.
X. Chen Regional Studies in Marine Science 43 (2021) 101674

Fig. 5. Comparison of measured and simulated salinities at the SE Fork Homosassa Spring, Homosassa Springs at Homosassa Spring, Halls River at Homosassa Spring,
Halls River near Homosassa, and Homosassa River at Homosassa stations during 1/5/2015 through 3/5/2015.

Table 1
MEs, MAEs, RMSEs, NRMSEs, R2 values, and Willmott skill assessment parameters for simulated water levels, salinities, and
temperatures, in comparison with real-time field data measured at the five stations within the simulation domain during the
calibration period, the verification, and the entire simulation period (11/4/2014–8/31/2017.)
Simulation Period ME MAE RMSE NRMSE R2 Skill
Water Level (cm)
Calibration −1.53 5.44 7.17 0.04 0.86 0.96
Verification 0.79 5.68 7.29 0.04 0.86 0.96
Calib. + Verif. −0.64 5.54 7.21 0.03 0.86 0.96
Salinity (psu)
Calibration −0.07 0.39 0.69 0.03 0.85 0.96
Verification 0.14 0.61 1.01 0.04 0.81 0.95
Calib. + Verif. 0.00 0.46 0.81 0.03 0.83 0.95
Temperature ()
Calibration −0.18 0.70 1.02 0.04 0.93 0.98
Verification −0.07 0.59 0.89 0.03 0.93 0.98
Calib. + Verif. −0.14 0.66 0.98 0.03 0.93 0.98

MEs for the temperature prediction by the LAMFE model are
−0.18, −0.07, and -0.14 ◦ C, respectively during the calibration,
verification, and entire periods. The corresponding MAEs during
the three periods are 0.70, 0.59, and 0.66 ◦ C, respectively. RMSEs
between simulated and measured temperatures are 1.02, 0.89,
and 0.98 ◦ C during the calibration, verification, and entire periods,
respectively, with their NRMSEs being consistent with those for
predicted water levels and salinities; namely about 0.03–0.04
for the three simulation periods. The R2 values between simu-
lated and measured temperature are 0.93 for all three simulation
periods, during which the Skills are all 0.98.
8
In summary, different assessments of the model skill show
that the LAMFE model performed very well for the simulation
of hydrodynamics, salinity transport processes, and thermal dy-
namics in the Homosassa system. If measured data at the USGS
stations at all real-time stations within the simulation domain of
the Homosassa River estuary were all perfectly accurate, statis-
tics listed in Table 1 would represent errors or uncertainties of
simulated water levels, salinities, and temperatures by the LAMFE
model. These errors or uncertainties are combined results of all
uncertainties in input data, model parameters, and numerical
X. Chen
Fig. 6. Comparison of measured and simulated temperatures at the SE Fork Homosassa Spring, Homosassa Springs at Homosassa Spring, Halls River at Homosassa
Spring, Halls River near Homosassa, and Homosassa River at Homosassa stations during 1/5/2015 through 3/5/2015.
schemes used in the model and they are all within acceptable
ranges.
4. Effects of SGD on salinity habitats
With the LAMFE model being well calibrated and verified,
effects of the SGD reduction on salinity habitats were investi-
gated by conducting a series of simulations with various flow
conditions, including the existing flow condition, a baseline flow
condition, and 12 flow reduction scenarios, ranging from 2.5%
reduction to 30% reduction with a constant 2.5% increment. The
baseline flow condition is an imaginary flow condition that would
exist if no ground water were withdrawn in the springshed. It
is estimated that the existing withdrawal causes about 1.85%
reduction of SGDs entering the Homosassa River estuary. As such,
the baseline flow is obtained by dividing the existing SGDs by
0.9815.
It is desirable to run the Homosassa River LAMFE model for
various flow reduction conditions for as many years as possible,
if input data which are used to drive the model are available. In
this study, the critical data needed for conducting simulations for
multiple years are the downstream boundary conditions. With
an effort to fill gaps in measured data based on available water
level, salinity, and temperature data in the GOM not far from
the mouth of the Homosassa River, the boundary conditions at
the downstream open boundary of the simulation domain be-
came available for a 125-month period from October 9, 2007 to
March 12, 2018, allowing a continuous simulation for more than
10 years. Details on the gap filling in the downstream boundary
9
Regional Studies in Marine Science 43 (2021) 101674
conditions and other data which drive the LAMFE model for the
125-month simulations can be found in Chen (2019a).
As the ecological health of the estuary depends on salinity
distributions in the waterbody, it is important to ensure that
the estuarine system has a proper salinity gradient along the
water course. Salinity habitats have been used as surrogate in
water resource regulations (Flannery et al., 2007; Ghile et al.,
2020; Murphy and Weiland, 2014; Fish and Wildlife Service,
2008; Rose et al., 2013). Plenty of water volumes of different
salinity zones are critical for various fish species. Generally, three
types of fish species exist in a healthy estuary, including freshwa-
ter, estuarine-resident, and estuarine-dependent species (Peebles,
2005). Freshwater fishes inhabit the tidal freshwater zones and
the upstream non-tidal segments of the estuarine system. Many
freshwater fishes also migrate into and feed in low salinity wa-
ters, as many of them can tolerate some amount of salt for
a short time (Peterson and Meador, 1994). Estuarine-resident
species spend their entire life cycle in the estuary and often have
broad salinity tolerances, but they do not migrate away from
the tidal river for feeding or reproduction. Estuarine dependent
species typically spend a portion of their early life cycle in the
estuary, with a later return to higher salinity coastal waters as
they mature. They include many fish and shellfish species of sport
or commercial importance in coastal areas.
While sufficient water volumes of different salinity zones
are needed for various fish types, changes in the bottom areas
of salinity zones are important to the distribution of benthic
macroinvertebrate communities, as different communities have
different levels of salinity tolerance. As such, both water volumes
X. Chen
Fig. 7. Time series of water volume, bottom area, and shoreline length of salinity ≤ 2 psu for 0%, 10%, 20%, and 30% reductions from the baseline flow conditions
in the Homosassa River estuary during September 3, 2011 through August 27, 2012.
and bottom areas of various salinity zones should be evaluated
in the ecological assessment of the estuary. In addition, shoreline
lengths of various salinity zones should also be evaluated, as their
distributions are correlated with different vegetation types.
In this study, water volumes, bottom areas, and shoreline
lengths of salinity ≤ 1, 2, 3, 5, 10, and 15 psu were calculated
using a post-processing program from simulated salinities in all
grid cells that were written out hourly. As mentioned before,
except for days near the end of the dry season, salinity at the
mouth of the Homosassa River estuary is generally lower than 25
psu. Water volume, bottom area, and shoreline length habitats for
salinity ≤ 20 psu represent most of the entire estuary. As a result,
salinity zones with higher upper limits (e.g., ≤20 or 25 psu) are
not as sensitive to the SGD as those of lower salinity zones and
are not included in the following discussion.
Figs. 7 and 8 are time series of simulated water volumes,
bottom areas, and shoreline lengths for salinity ≤ 2 and 10
psu, respectively during September 3, 2011 through August 27,
2012 under the baseline flow condition and three flow reduction
conditions: 10%, 20%, and 30%. The top panels in the figures are
water volumes, while middle and bottom panels are respectively
bottom areas and shoreline lengths of the corresponding salinity
zones. For simplicity, only a randomly selected 360-day period
are shown in the figures, though flow scenarios were run for a
simulation period of more than ten years. For the same reason,
10
Regional Studies in Marine Science 43 (2021) 101674
only salinity ≤ 2 and 10 psu and only four flow conditions are
presented here in the figures. Time series plots of salinity habitats
for other salinity zones and flow scenarios can be found in Chen
(2019a), though they are presented in a different way.
As shown in Fig. 7, ≤2 psu water volumes varied within a
range roughly between 20,000 m3 and 1 million m3 , while ≤2 psu
bottom areas varied from about 20,000 m2 to about 1 million m2
during the 360 days. The ≤2 psu shoreline length was roughly
between 300 m and 15,000 m. When the baseline flow was
decreased by 10%, 20%, and 30%, ≤2 psu water volume, bottom
area, and shoreline length were decreased accordingly at each
time point, with all the peaks being evidently reduced for all three
salinity habitats.
Simulated salinity habitats for salinity ≤10 psu ranged approx-
imately between 1.6 and 9.0 million m3 , 1.0 and 5.5 million m2 ,
and 20 to 78 km for water volume, bottom area, shoreline length,
respectively. The relative variabilities of ≤10 psu salinity habitats
are much smaller than those of ≤2 psu salinity habitats. Salinity
habitats of ≤10 psu are not very sensitive to an SGD reduction
most of the year; however, during the dry season, starting in late
April and ending in late June, when the region generally receives
the least rainfall of the year, the effect of an SGD reduction on the
availability of ≤10 psu salinity habitats becomes noteworthy.
Both the ≤2 and 10 psu salinity habitats show seasonal vari-
abilities. During the wet season, there exist much more ≤2 and
X. Chen
Fig. 8. Time series of water volume, bottom area, and shoreline length of salinity ≤ 10 psu for 0%, 10%, 20%, and 30% reductions from the baseline flow conditions
in the Homosassa River estuary during September 3, 2011 through August 27, 2012.
10 psu salinity habitats than during the dry season. Because tidal
signals are included not only in the downstream boundary con-
ditions but also in the upstream SGDs, simulated water volume,
bottom area, and shoreline length for any salinity zones also con-
tain tidal signals with both diurnal and semidiurnal variabilities.
From Figs. 7 and 8, the diurnal and semidiurnal signals in the
simulated salinity habitats are weaker than those of weekly vari-
abilities, about one half of the spring–neap cycle. This is different
from other estuaries, where freshwater inflows are mainly from
surface water runoff and thus no tidal signals in the hydrologic
loading. For the Homosassa River, because SGDs are affected
by tides, effects of tides on salinity habitats are enhanced and
generally much stronger than these in estuaries without SGD
being the major source for hydrologic loading.
Direct comparisons and analyses of hourly model results of
water volume, bottom area, and shoreline length for different
flow reductions are very tedious and not necessary, because one
would easily lose the forest for the trees. While the temporal
variation of salinity zones in the estuary may have a time scale
of hours or days, the time scale of the response of various species
to salinity changes is normally much longer. As such, cumulative
distribution functions (CDFs) of salinity habitats are often gener-
ated and analyzed to get an overall picture of the effects of flow
reductions on salinity habitats (Flannery et al., 2007; Ghile et al.,
2020).
11
Regional Studies in Marine Science 43 (2021) 101674
Figs. 9–11 are CDFs of water volume, bottom area, and shore-
line length for various salinity zones and flow reduction scenarios.
For a better inspection of the differences among different CDFs
for different flow reductions, only the baseline, existing, 2.5%, 5%,
10%, 15%, 20%, 25%, and 30% flow reduction scenarios are included
in Figs. 9–11. From these figures, it is apparent that habitats of
lower salinity zones are generally more sensitive to a flow change
than those of higher salinity zone. For example, CDF curves for
≤15 psu water volume, bottom area, and shoreline length are
only altered slightly for different flow scenarios, but CDF curves
for ≤2 psu are changed significantly under different flow con-
ditions. This property is consistent with other estuarine systems
evaluated in southwest Florida, which receive hydrologic loadings
mainly from surface water runoff. In other words, regardless of
the source of freshwater inflow or if the inflow contains tidal
signals, lower salinity habitats are more sensitive than those of
other salinity zones. Nevertheless, there is an exception for the
Homosassa River, where salinity habitats of ≤1 psu is not very
sensitive to SGD reductions. The reason for the relatively weak
sensitivity of ≤1 psu salinity habitats to flow is that these near
freshwater habitats are mainly found in the SE Fork of the river
(Fig. 12), which contributes less than half of the total hydrologic
loading to the estuary. On the other hand, the Halls River receives
SGDs that are much saltier than SE Fork SGDs. As mentioned
before, SGDs entering the Hall River are to some degree salinity
X. Chen
Fig. 9. Cumulative distribution functions of simulated water volumes for various flow reductions for salinity ≤ 1, 2, 3, 5, 10, and 15 psu.
source for the Hall River and thereby for the entire estuary.
Because SGDs from all the spring vents are reduced by the same
percentage from the baseline condition in the flow reduction
simulations, saltier water inflow to Halls River was reduced while
freshwater inflow to the SE Fork was reduced. The combined
effect is the relatively weak sensitivity of ≤1 psu salinity habitats
to the SGD.
From Figs. 9–11, one can see that ≤2 and 3 psu salinity
habitats within the middle half of the range are much more
sensitive to an SGD reduction than those above the 90th per-
centile, which occurs mainly during the wet season. While ≤2 psu
salinity habitats are most sensitive to an SGD reduction near the
70th percentile, ≤3 psu salinity habitats are most sensitive near
the 25th percentile. For ≤5 psu salinity habitats, they are most
sensitive at near the 85th percentile; however, the most sensitive
≤10 psu salinity habitats occur near the 15th percentile. Such a
response of salinity habitats to an SGD reduction is associated
with the location of the individual salinity isohaline, which varies
depending on the tides and salinity at the downstream bound-
aries as well as SGDs received. To this end, the physical setting of
the Homosassa River also plays a big role influencing the salinity
isohaline and the response of the salinity habitats.
12
Regional Studies in Marine Science 43 (2021) 101674
Fig. 12 is a map showing the long-term mean of simulated
depth-averaged salinity during the 125-month simulation period
for the baseline flow condition in the estuary. Although the actual
salinity distribution varies with time, Fig. 12 provides some gen-
eral information about the area of different salinity zones most
of time in the estuary. The 2 psu isohaline is generally located
upstream of the confluences of Halls River with the Homosassa
River, while the 3 psu isohaline moves within a segment down-
stream of the Halls River confluence. One can see that there
is narrow transect downstream of the Halls River confluence,
where the Homosassa River becomes not only deeper but also
much wider as one travel from upstream to downstream. This
bathymetric change affects the sensitivity of the ≤2 and 3 psu
water volumes and bottom areas to the SGD. In Fig. 9, one can
see that the 70th percentile of ≤2 psu water volume is about
1.1 million m3 , which is about the same as the 25th percentile
of ≤3 psu of water volume. Similarly, one can see in Fig. 10 that
the 70th percentile of ≤2 psu bottom area is about 0.65 million
m2 , which is roughly the same as the 25th percentile of ≤3 psu
bottom area. In other words, the 70th percentile of ≤2 psu and
the 25th percentile of ≤3 psu represent approximately the same
X. Chen
Fig. 10. Cumulative distribution functions of simulated bottom areas for various flow reductions for salinity ≤ 1, 2, 3, 5, 10, and 15 psu.
area of the estuarine system, which includes a short downstream
segment of the Halls River and all the areas of the Homosassa
River that are upstream of the narrow cross section located just
downstream of the Halls River confluence.
The 5 psu contour isohaline is generally located near the
town Homosassa. During the dry days, it can migrate toward the
Halls River confluence; however, during the wet days, it can be
pushed to cross sections downstream of the town Homosassa and
into several distributaries that branch off the Homosassa River,
including the Salt River and Mason Creek. On the other hand,
the 10 psu isohaline generally occurs downstream of these dis-
tributaries. In relatively dry days, the 10 psu isohaline will retreat
toward the town Homosassa and into the distributaries. It turns
out that these distributaries can cause ≤5 and 10 psu salinity
habitats to be very sensitive to a flow reduction. With about at 6.0
million m3 , 3.4 million m2 , and 50 km of water volume, bottom
area, shoreline length respectively, the 85th percentile of ≤5 psu
salinity habitats cover basically the same area of the estuary as
that of the 15th percentile of ≤10 psu salinity habitats. At these
numbers, an SGD increase or decrease would cause the most
relative increase/decrease for ≤5 and 10 psu salinity habitats.
13
Regional Studies in Marine Science 43 (2021) 101674
To quantify the long-term changes of salinity habitats caused
by a flow reduction, average water volume, bottom area, and
shoreline length for different salinity zones can be calculated over
the entire 125-month period. Numerically, these average values
are equal to areas between the y-axis and the corresponding
CDF curves shown in Figs. 9–11. Averages of ≤1, 2, 3, 5, 10,
and 15 psu salinity water volumes, bottom areas, and shoreline
lengths for various SGD reductions are plotted in Fig. 13. As
can be seen from the figure, no obvious refection points can be
found in these curves representing relationships between salinity
habitats and the percentage SGD reduction and the relationships
are practically linear. With a linear regression, the R2 values of
the linear model are all higher than 0.99, except for ≤1 salinity
water volume, bottom area, and shoreline length, which have R2
values of 0.97, 0.96, and 0.96, respectively. The slope of each re-
gression line represents response of the long-term average of the
simulated salinity habitat to an SGD change. Using the long-term
averages of simulated water volume, bottom area, or shoreline
length for salinity ≤ 1, 2, 3, 5, 10, and 15 psu under the baseline
flow condition to normalize the slopes, normalized response rates
can be calculated and listed in Table 2. In the table, BLV denotes
X. Chen Regional Studies in Marine Science 43 (2021) 101674

Fig. 11. Cumulative distribution functions of simulated shoreline length for various flow reductions for salinity ≤ 1, 2, 3, 5, 10, and 15 psu.

Table 2
Simulated salinity habitats under the baseline flow condition (BLV) and normalized response rate
for different salinity zones in the Homosassa River estuary.
Salinity zone Water volume Bottom area Shoreline length
BLV (mil m3 ) NRR BLV (mil m2 ) NRR BLV (km) NRR
≤1 psu 0.02 0.41 0.02 0.31 1.62 0.25
≤2 psu 0.47 1.38 0.32 1.38 6.73 0.96
≤3 psu 1.00 1.22 0.73 1.25 13.85 1.02
≤5 psu 1.95 1.00 1.52 1.01 28.42 0.92
≤10 psu 3.85 0.43 3.05 0.42 54.32 0.38
≤15 psu 5.30 0.15 4.11 0.14 68.62 0.11

the 125-month average of simulated water volume, bottom area,
or shoreline length for any of the salinity zones under the baseline
flow condition, while NRR is the normalized response rate, a
dimensionless parameter representing the sensitivity of salinity
habitats to the SGD change.
From Table 2, it can be seen that except for the ≤1 salinity
habitats, the sensitivity of the simulated salinity habitat decreases
as the upper limit of the salinity zone increases. For example, the
NRR for ≤2 psu water volume is 1.38, while NRR for ≤10 psu
water volume is 0.43. In other words, every 1% of SGD change
14
will cause 1.38% change of ≤2 psu water volume but only 0.43%
change of ≤10 psu water volume. Generally, oligohaline habitats
in the Homosassa River estuary increase/decrease roughly 1% or
more with a 1% increase/decrease of SGD. However, as the salinity
zone is expanded to include mesohaline, the sensitivity becomes
weaker and weaker. The most sensitive salinity zones are ≤2 psu
for the water volume and bottom area. For the shoreline length, it
is the ≤3 psu salinity zone the most sensitive to an SGD change.
The ≤2 psu water volume and bottom area are also the most
sensitive among all the salinity habitats studied here.
X. Chen Regional Studies in Marine Science 43 (2021) 101674

Fig. 12. Depth-averaged, 125-month mean salinity distribution during October 9, 2007 to March 12, 2018 in the Homosassa River for the baseline flow condition.
White contour lines are spaced with a 1 psu interval.

Fig. 13. Relationships of salinity habitats with SGD reduction in the Homosassa River Estuary. Sal_1, Sal_2, Sal_3, Sal_5, Sal_10, and Sal_15 in the legends represent
salinity ≤ 1, 2, 3, 5, 10, and 15 psu.

From Table 2, one can see that the water volume and bottom
for each of the salinity zone have about the same NRR, which
is generally higher than that for the shoreline length in the
Homosassa River estuary. This is slightly different from other es-
tuaries in southwest Florida, where the water volume of a salinity
zone is generally more sensitive to the freshwater inflow than the
bottom area of the same salinity zone, which is more sensitive
than the shoreline length. The reason for such a response is that
water volume, bottom area, and shoreline length of a salinity
zone are respectively three-, two-, one-dimensional functions of
15
length in these other estuaries. In the Homosassa River, however,
the estuary is shallow and except for the navigation channel and
some deep holes, most riverbed varies between a small range
around 0.5 m deep. Because the estuary is generally well-mixed,
the water volume of a salinity zone varies in a similar way as
the bottom area and both are just two-dimensional functions of
length. As such, the water volume and bottom area for the same
salinity zone have roughly the same sensitivity to an SGD change.
X. Chen
5. Conclusions
The laterally averaged hydrodynamic model LAMFE was ap-
plied to the Homosassa River estuary to simulate circulations,
salinity transport processes, and thermal dynamics in the spring-
fed estuary on the Gulf coast of Florida peninsula. SGDs received
by the estuary were either recorded at proper transects down-
stream of spring vents using ADCPs or estimated using regression
equations relating spring flows with tides and groundwater levels
in the region. The model was calibrated and verified against real-
time data of water level, salinity, and temperature collected at
five stations within the simulation domain. Various skill assess-
ments were conducted and have shown that the LAMFE performs
very well for the spring-fed estuary.
As many estuarine species depend on the availability of differ-
ent salinity zones, salinity habitats, especially oligohaline salinity
habitats, which are often used as surrogate for determining the
health of the estuary, need to be protected. For this purpose, this
study investigated the impact of reduced SGDs on the salinity
habitats in the Homosassa River using the calibrated/verified
LAMFE model. Salinity habitats considered here included ≤1, 2,
3, 5, 10, and 15 psu water volumes, bottom areas, and shoreline
lengths.
Model results show that different salinity habitats respond to
the SGD differently in the Homosassa estuary. Over the short
term, the response is greatly affected by some special physical
features of the waterbody and the SGD that the estuarine system
receives. The sensitivity of the instantaneous salinity habitat to
the SGD varies with the location of the isohaline (and thereby the
percentile of the habitat) in relationship with these physical fea-
tures. For example, the response of ≤2 and 3 psu salinity habitats
is affected by a cross section change, which is a short distance
downstream of the Halls River confluence with the Homosassa
River. For ≤5 and 10 psu salinity habitats, their sensitivities are
affected by the distributaries located downstream of the town
Homosassa.
Model results also show that long-term averages of salinity
habitats in the Homosassa River are linearly decreased with an
increasing SGD reduction percentage. Normalized response rates
to an SGD change were calculated for all the salinity zones con-
sidered in order to quantify sensitivities of different salinity zone
to the SGD. It was found that water volumes and bottom areas of
the same salinity zone are similarly sensitive to an SGD change
and both are more sensitive than the shoreline length. Except for
those of ≤1 psu, oligohaline salinity habitats are more sensitive
to SGD than higher salinity zones. Salinity habitats for ≤2, 3, and
5 psu linearly increase/decrease about 1% or more with every 1%
increase/decrease of SGD. The ≤2 psu water volume and bottom
area are the most sensitive habitats to a SGD change and they are
reduced about 1.38% for every 1% reduction of the SGD.
Declaration of competing interest
The authors declare that they have no known competing finan-
cial interests or personal relationships that could have appeared
to influence the work reported in this paper.
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