Limnol. Oceanogr.

9999, 2024, 1–16

Published 2024. This article is a U.S. Government work and is in the public domain in the
USA. Limnology and Oceanography published by Wiley Periodicals LLC on behalf of
Association for the Sciences of Limnology and Oceanography.
doi: 10.1002/lno.12549

Deep learning of estuary salinity dynamics is physically accurate at a

fraction of hydrodynamic model computational cost
Galen Gorski ,1* Salme Cook ,2 Amelia Snyder ,1 Alison P. Appling ,3 Theodore Thompson ,4
Jared D. Smith ,1 John C. Warner ,2 Simon N. Topp 1
1
U.S. Geological Survey, Reston, Virginia, USA
2
U.S. Geological Survey, Woods Hole Coastal and Marine Science Center, Woods Hole, Massachusetts, USA
3
U.S. Geological Survey, State College, Pennsylvania, USA
4
U.S. Geological Survey, Lawrenceville, New Jersey, USA

Abstract
Salinity dynamics in the Delaware Bay estuary are a critical water quality concern as elevated salinity can
damage infrastructure and threaten drinking water supplies. Current state-of-the-art modeling approaches use
hydrodynamic models, which can produce accurate results but are limited by significant computational costs.
We developed a machine learning (ML) model to predict the 250 mg L
1 Cl
isochlor, also known as the “salt
front,” using daily river discharge, meteorological drivers, and tidal water level data. We use the ML model to
predict the location of the salt front, measured in river miles (RM) along the Delaware River, during the period
2001–2020, and we compare predictions of the ML model to the hydrodynamic Coupled Ocean–Atmosphere-
Wave-Sediment Transport (COAWST) model. The ML model predicts the location of the salt front with greater
accuracy (root mean squared error [RMSE] = 2.52 RM) than the COAWST model does (RMSE = 5.36); how-
ever, the ML model struggles to predict extreme events. Furthermore, we use functional performance and
expected gradients, tools from information theory and explainable artificial intelligence, to show that the ML
model learns physically realistic relationships between the salt front location and drivers (particularly dis-
charge and tidal water level). These results demonstrate how an ML modeling approach can provide predictive
and functional accuracy at a significantly reduced computational cost compared to process-based models. In
addition, these results provide support for using ML models in operational forecasting, scenario testing, man-
agement decisions, hindcasting, and resulting opportunities to understand past behavior and develop
hypotheses.

In the mid-Atlantic region of North America, the Delaware
River Basin supplies drinking water for 15 million people
including nearly half of the population of New York City
(Hutson et al. 2016). Water resources in the basin are jointly
managed by four states and the federal government to meet
demand while also maintaining downstream flow and water
*Correspondence: ggorski@usgs.gov
This is an open access article under the terms of the Creative Commons
Attribution License, which permits use, distribution and reproduction in
any medium, provided the original work is properly cited.
Additional Supporting Information may be found in the online version of
this article.
Author Contribution Statement: AA, JW, GG, and JS all helped con-
ceive the study and secure support. GG, SC, AS, and TT executed the
study, and GG, SC, JS, AA, and ST analyzed and interpreted the results.
JS and ST made methodological contributions to the analysis. GG, SC, JS,
and AA wrote the manuscript, while AS, TT, ST, and JW contributed to
the editing and revision of the manuscript and figures.
quality objectives (Mandarano and Mason 2013). Within the
Delaware River Basin, the main stem of the Delaware River pro-
vides recreational opportunities, critical habitat to endemic spe-
cies, and drinking water for several urban areas including
Philadelphia, Pennsylvania. Salinity concentrations within the
lower reaches of the Delaware Bay estuary vary throughout the
year, but during periods of low river discharge, ocean salinity
can be driven upstream, threatening water quality. Increased
salinity conditions, which can be brought on by drought, sea
level rise, and/or increased demand, can corrode critical infra-
structure, threaten species habitat, and necessitate further treat-
ment or alternative sources of drinking water. As such, salinity
is a key constituent in the Delaware Bay estuary, and its dynam-
ics are tracked closely to ensure the protection of water quality.
For example, managed releases from upstream reservoirs, which
are jointly managed for drinking water, flood control, recrea-
tion, and other purposes, are used to meet minimum flow
objectives and manage salinity intrusion. However, these
releases require the careful balancing of salinity mitigation with

1

Gorski et al.
other beneficial uses, and there is considerable uncertainty sur-
rounding the effect that the timing and magnitude of releases
have on downstream salinity.
Within the Delaware Bay estuary, salinity intrusion is measured
using the location of the 7-d average 250 mg L
1 Cl
isochlor,
also referred to as the “salt front.” The location of the salt
front is reported in river miles (RM; 1.6 km) along the central
axis of the estuary, ranging from 0 at the mouth of the estu-
ary to 134 at Trenton, NJ where the river is no longer
influenced by ocean tides. The location of the salt front, and
salinity dynamics more broadly, in the Delaware Bay estuary
are primarily controlled by river discharge along the
mainstem of the Delaware River and from other major tribu-
taries such as the Schuylkill River. However, other factors
such as tidal action, meteorological systems, and bathymetric
and topographical features also have influence, particularly
during times of low discharge (Ross et al. 2015).
Current models of the Delaware Bay estuary primarily use
numerical techniques to solve equations for the fundamental
physical processes which drive salinity, hydrologic, and other
biogeochemical dynamics (Galperin and Mellor 1990a,b;
Whitney and Garvine 2006; Aristazabal and Chant 2013; Phil-
adelphia Water Department 2015). For example, the Coupled
Ocean–Atmosphere-Wave-Sediment Transport (COAWST)
modeling system has been used to accurately simulate salinity
dynamics in the Delaware Bay (Cook et al. 2023).
While numerical hydrodynamic models such as COAWST
can accurately simulate water level, temperature, salinity, and
other constituents at fine spatial and temporal resolutions
(Warner et al. 2010), there are substantial drawbacks including:
(1) high computational costs in running the model, which can
lead to long run times, shorter simulation periods, and diffi-
cultly in using the model for operations or short-term forecast-
ing. For example, the COAWST model takes  50 h of compute
time on 180 processors to simulate 1 yr of conditions within
the Delaware Bay estuary. This limits the ability to test suites of
scenarios simulating reservoir releases or potential future condi-
tions. In addition, given the computational constraints, produc-
ing model ensembles for uncertainty or using ensemble-based
data assimilation approaches to develop operational models for
near-term forecasting is not feasible; (2) substantial system-
specific expertise required to define boundary conditions and
configure the model; (3) significant requirements for hosting
and accessing input and output data due to fine spatial and
temporal resolutions of the model, for example, the COAWST
model outputs  2 TB of data for a single year of simulations.
The rapid advances of machine learning (ML) have shown
great promise in simulating dynamics in complex environmental
and hydrologic systems, including estuaries, at reduced computa-
tional costs (Zaini et al. 2022; Bahari et al. 2023; Qi et al. 2023).
For example, Zhou et al. (2021) used the Cubist ML algorithm to
estimate the impact of Mississippi River discharge on estuary
salinity dynamics along the Gulf Coast. Alizadeh et al. (2018)
showed that ML models could accurately forecast estuarine water
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Deep learning model of Delaware Bay
quality constituents, including salinity, up to 2 h in the future
(Alizadeh et al. 2018). Other studies have demonstrated how ML
models can reduce cost in data collection and computation
(Codden et al. 2021). The flexibility and computational efficiency
of such models raises exciting possibilities about their capacity to
harness ever-growing data availability to develop accurate models
at speeds and resolutions not possible with traditional modeling
approaches. However, the complexity of ML models’ inner work-
ings can make it difficult to discern if the models are representing
a system in a physically reasonable way. Moving beyond purely
predictive performance metrics, it is important to ensure that ML
models are getting the right answers for the right reasons
(Kirchner 2006). This issue is particularly critical if models are to
be used for forecasting, testing of future scenarios, or extrapola-
tions of any kind in space and/or time.
This type of model accuracy is termed functional performance,
which represents the ability of a model to accurately reproduce
coupling and sensitivities within the system (Ruddell et al. 2019).
A model with high functional performance should reproduce
pairwise input–output relationships seen in the observed data.
Transfer entropy, a metric from information theory, has been
proposed as a method for assessing functional performance, as
it provides a robust measure of non-linear, one-way coupling
between inputs and outputs (Schreiber 2000; Ruddell and
Kumar 2009; Konapala et al. 2020). The joint assessment of pre-
dictive and functional performance can provide a deeper under-
standing of a model’s ability to represent a physical system and
help identify potential weakness in the model.
The ML model used in this study is a long short-term memory
(LSTM) network (Hochreiter and Schmidhuber 1997), a kind of
temporally aware neural network that has shown skill in rep-
resenting hydrologic processes due to its ability to retain informa-
tion over many time steps (Rahmani et al. 2020; Frame
et al. 2021; Zhi et al. 2021). As the name suggests, the network is
engineered to discern which information from the past is relevant
to the current time step and to carry that information forward.
This behavior has natural resonance with hydrologic systems,
where storage and transfer can operate across a range of different
scales. An advantage of LSTMs is that they can identify these
timescales from input data automatically (Tennant et al. 2020).
In this study, we develop a ML model to predict the 7-d
backward-looking average salt front location using daily obser-
vations of discharge, meteorological variables, and water levels.
We train the model using a record of the salt front location
from 2001 to 2020 developed by the Delaware River Bay Com-
mission (Preucil and Reavy 2020) with data from 2001 to 2015
used for training and 2016 to 2020 used for testing. We com-
pare the model results with modeled salt front location from
the COAWST hydrodynamic model for 3 yr during the holdout
period for which we have results for both models. In addition
to comparing predictive performance of the two models, we
use transfer entropy between river discharge and salt front
location to compare model functional performance at identi-
fied critical time scales. As COAWST is a state-of-the-art

Gorski et al.
hydrodynamic model (Warner et al. 2010), it serves as a point
of comparison for measuring the predictive and functional per-
formance of the ML model. We also investigate the ML model’s
internal gradients using a method called expected gradients
(EGs) (Erion et al. 2021) to assess whether the model is using
input variable data in a physically consistent manner.
The reduced computational cost and increased flexibility of
ML approaches raise the possibility of quickly running ensem-
bles of scenarios. These applications would have the potential to
inform water resources management both in real time and for
the long term. For this and other future applications to be real-
ized, modeling frameworks need to be rigorously compared to
both observational data and the existing state-of-the-art model-
ing approaches to understand their strengths and weaknesses.
Although ML approaches have been applied to estuary salinity
in the past, this work focuses on explicitly comparing state-of-
the-art process-based modeling to ML methods using a combina-
tion of predictive and functional performance metrics. In
addition, our use of EGs to examine the drivers of model
response through time is a unique application of this explainable
artificial intelligence technique to understand model behavior.
Materials
Geographical setting
The Delaware Bay estuary is a coastal plain estuary that drains
an area of about 35,000 km2 across Pennsylvania, New Jersey,
New York, Delaware, and Maryland (Hutson et al. 2016). The
Delaware River, its main tributary, contributes  60% of the
annual freshwater to the total discharge of the estuary, with
the Schuylkill River contributing an additional 15% and no other
single tributary contributing more than 1% (Sharp et al. 1986)
(Fig. 1). Streamflow is highest in the spring and lowest in the late
summer and early fall (Supporting Information Fig. S1).
Salinity dynamics within the estuary have been character-
ized as having a weak response to variation in streamflow
compared to other estuary systems (Garvine et al. 1992;
Aristazabal and Chant 2013). This is in large part due to signif-
icant tidally driven advection dominated by the M2 principal
lunar constituent (Wong 1995), vertical mixing, and the shape
of the estuary. Other factors such as wind and gravitational
flow due to density gradients formed by freshwater inputs can
also affect salinity dynamics (Galperin and Mellor 1990a).
Throughout the estuary, lateral variations in salinity are gener-
ally greater than vertical (Wong and Münchow 1995), with more
saline water found in the middle of estuary. These lateral gradients
are likely less important in the upper reaches of the estuary, as it
narrows considerably (Sharp et al. 1982). While lateral salinity gra-
dients can be important for driving salinity dynamics in certain
parts of the estuary, they are beyond the scope of this study.
Data sources
The ML model uses daily dynamic drivers to make predic-
tions: discharge at two locations, four meteorological variables
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Deep learning model of Delaware Bay
(barometric pressure, air temperature, wind direction, and
wind speed), and four tidal signatures, for a total of
10 predictors. Daily river discharge data were acquired from
the Delaware River at Trenton, NJ (USGS Site 01463500) and
Schuylkill River at Philadelphia (USGS Site 01474500) using
the USGS National Water Information System (U.S. Geological
Survey 2022). Daily meteorological data were downloaded
from the NOAA National Estuarine Research Reserve System
(NERRS) at Saint Jones River (DELSJMET) (NOAA NERRS n.d.)
(Fig. 1). We used the Saint Jones River data because that sta-
tion provided the only complete record of all variables of
interest among stations in the area, and the station record is
more locally accurate than a gridded meteorological product.
Observed and predicted water level data from the mouth of
the estuary were downloaded from the NOAA National Ocean
Service (NOS) Tides and Currents web portal for Lewes, DE
(8557380) at a 6-min resolution (NOAA National Ocean
Services n.d.). Water levels are predicted for specific locations
along the coastline using celestial mechanics and past local
observations (NOAA Center for Operational Oceanographic
Products and Services n.d.). Water level data was converted
from 6-min resolution to the daily time step by calculating
the daily range, maximum height, difference between
predicted and actual height, and subtidal frequency fluctua-
tions (Supporting Information Material Data preprocessing).
The ML model target variable is the backward-looking 7-d
average location of the 250 mg L
1 Cl
isochlor, known as the
salt front. The salt front location in units of RM is a specific reg-
ulatory metric, as such our modeling and analysis is done in
these units (Delaware River Basin Commission 2019). The loca-
tion of the salt front is estimated by the Delaware River Basin
Commission using daily observations of specific conductivity
from four locations throughout the estuary, Reedy Island
(RM 54), Chester (RM 84), Fort Mifflin (RM 92), and the Ben
Franklin Bridge (RM 100). Specific conductivity is converted to
Cl
using a locally calibrated conversion, and a log-linear inter-
polation method is used to estimate Cl
concentration between
observation points (Preucil and Reavy 2020). When station data
is missing due to a faulty sensor or routine maintenance, often
in the winter months, a correction is applied to interpolate
between non-adjacent sensors. Uncertainty estimates are not
available for the salt front location. For the purposes of calculat-
ing the salt front from observations, salinity is synonymous
with Cl
concentration.
The 7-d average salt front is similar to the position of the
2 g kg
1 isohaline (X2) used as a measure of salinity intrusion
in other estuaries (Guerra-Chanis et al. 2019). It is an advanta-
geous target variable for several reasons. First, it is a
management-relevant variable that is directly referenced in
decisions to mitigate salinity by releasing water from upstream
reservoirs (U.S. Geological Survey, Office of the Delaware River
Master 2017). Second, in contrast to an Eulerian frame of ref-
erence such as salinity concentration at single or multiple
locations, a time series of the salt front location describes the
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Gorski et al. Deep learning model of Delaware Bay

Fig. 1. Map of study area. Orange bars indicate river mile intervals used for model performance analysis; yellow inverted triangles provide historical and
management context. Projection: World Geodetic System 1984. Basemap generated using the tigris and dataRetrieval packages in R (R Core Team 2022;
DeCicco et al. 2023; Walker 2023), depth data from (NOAA National Centers for Environmental Information 2005).

directional history of salinity within the estuary; it conveys
whether salinity is advancing inland or being repelled down-
stream. Finally, the salt front location is a single value that
provides a succinct summary of salinity conditions in the estu-
ary; more complex model output, such as maps of salinity or
salinity at several locations, would require post-processing to
produce similarly useful information. Although choosing an
interpolated value for the modeling target introduces addi-
tional uncertainty from the interpolation method that might
be avoided if we were instead to model salinity at several loca-
tions, we elected to select the salt front record as it is a target
with more management relevance.
ML model
To model the 7-d average location of the salt front we use the
LSTM ML method (Hochreiter and Schmidhuber 1997). The
LSTM is a type of temporally aware neural network that has been
used successfully to model complex hydrologic systems (Kratzert
et al. 2018; Read et al. 2019; Jia et al. 2021; Sadler et al. 2022). Its
success in hydrology over other ML methods is largely due to its
ability to represent system memory and antecedent conditions.
An LSTM is a sensible choice in this case as antecedent condi-
tions and system memory have strong influence on the salt front
movement (Supporting Information Fig. S1). The fundamental
unit of an LSTM is a cell or hidden unit, which is made up of a
series of gates through which incoming data pass. The gates con-
trol the flow of information throughout the model: the input
gate controls which information from the current time step is
added to the model’s memory, the forget gate controls which
information from the previous time step is removed from mem-
ory, and the output gate controls which information is used to
make the current time step’s prediction. The LSTM cells can be
represented in a simplified way by:
ht , ct ¼ f LSTM ðht
1 , ct
1 , xt Þ, ð1Þ
st ¼ f linear ðht Þ, ð2Þ
where h and c are the hidden state and cell state, respectively,
and xt represents a vector of the model inputs at time t. The
full set of equations describing the LSTM’s functions as well as

4

Gorski et al.
details describing the choice of modeling hyperparameters
and number of replicates can be found in the Supporting
Information.
In Eq. 2, the LSTM is used to generate the prediction of the
salt front location, st, using linear regression. We employed a
model with a single LSTM layer, 20 hidden units, a look back
sequence length of 365 d, dropout of 0.1 and a recurrent dropout
of 0.3. The model was trained for 500 epochs with a learning rate
of 0.003. The results presented are the average of 10 model repli-
cates differing only in the random initiation of model weights.
All input data were z-score normalized before modeling.
The modeling time period (2001–2020) was split into train-
ing (2001–2010), validation (2011–2015), and testing (2016–
2020) periods. To determine model hyperparameters a grid sea-
rch was used, and models were trained on data from the train-
ing period and assessed during the validation period
(Supporting Information Material). Once the hyperparameters
had been selected, the final model was trained using combined
data from the training and validation periods (2001–2015) and
assessed during the testing period. Model performance results
refer to the testing period unless otherwise stated.
COAWST hydrodynamic model
The COAWST modeling system (Warner et al. 2008, 2010)
was used to model the processes controlling salinity intrusion in
the Delaware Bay. The Regional Ocean Modeling System
(Haidvogel et al. 2000, 2008; Shchepetkin and McWilliams 2005)
was employed as the ocean circulation model. River discharge
was prescribed using the USGS gage at Trenton, NJ (USGS Site
01463500; U. S. Geological Survey 2022). Flows at the Chesa-
peake and Delaware Canal were estimated from NOAA water
level and velocity measurements at Chesapeake City, MD
(8573927; NOAA National Ocean Services n.d.). Tidal forcing
was from the Advanced Circulation Model (Mukai et al. 2001).
Subtidal forcing was generated using a 32-h low pass filter from
water level observations interpolated from Lewes, DE (8557380)
and Cape May, NJ (8536110). Temperature and salinity bound-
ary conditions at the coastal ocean are provided by the COAWST
forecast model (Warner and Kaira 2022). All model runs included
atmospheric dynamics that were forced by the European Center
for Medium-Range Weather Forecasts Reanalysis v5 (Hersbach
et al. 2020) with a spatial resolution of 30 km and a temporal res-
olution of 1 h. The COAWST model was calibrated using water
level and salinity at four stations. Details of the calibration
scheme can be found in (Cook et al. 2023).
The COAWST model simulates estuary water level, veloci-
ties, temperature, and salinity, among other output variables,
at a spatial resolution of 5–450 m. The model was simulated
with 16 vertical levels and run with a 2- to 10-s time step.
Several methods for comparison of COAWST model output to
ML simulations were considered, including selecting COAWST
salinity simulation from the locations where specific conduc-
tivity observations were collected and post-processing to inter-
polate a simulated salt front record. We elected to use the
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Deep learning model of Delaware Bay
method that had previously been employed by Cook et al.
(2023) and was the most likely to be used in a decision-
making context. To derive a time series of the modeled salt
front location from COAWST output, salinity is aggregated to
the daily timestep, and the bottom of the vertical cell equal
to approximately 0.52 psu (250 mg L
1 Cl
) is selected
(Philadelphia Water District 2019). Each model run consists of
simulating a specific year, and each year is run independently.
Note that the COAWST model and the ML model are designed
to predict different quantities at different spatial and temporal
resolutions and scales, therefore the models are not necessarily
on equal footing for different prediction tasks. However, in
this study, we have designed the comparison to emphasize rel-
evance from a management perspective.
Assessing model performance
The predictive performance of the hydrodynamic and ML
models were assessed against the salt front record using root
mean squared error (RMSE) and Nash–Sutcliffe efficiency (NSE)
(Nash and Sutcliffe 1970). The model performance was assessed
separately for a set of six RM intervals (< 58, 58–68, 68–70, 70–
78, 78–82, > 82 RM) using geographic and bathymetric control
points (Fig. 1). The intervals do not have the same length but
were chosen based on the physical structure of the system. The
features of the intervals are discussed in the Spatial Variability
in Modeling Results section of the Discussion.
The functional performance of the model is an indication
of how well a model represents the relationships between
inputs and outputs compared to the observed relationships.
To compute functional performance, we used transfer entropy
(TE), a concept from information theory that quantifies the
asymmetric flow of information between sources and sinks
and can capture both linear and non-linear interactions
(Schreiber 2000). The TEX!Y is a measure of the reduction in
uncertainty in Y (the sink variable) gained through knowledge
of X (the source variable), conditioned on the history of Y
(Schreiber 2000; Ruddell and Kumar 2009). In our analysis, we
focused on discharge from the Delaware at Trenton, NJ and
discharge from the Schuylkill at Philadelphia as the source var-
iables (Xj ) for transfer entropy calculations, where j is the
index of the source location, j is an element of fT, Sg for Tren-
ton or Schuylkill, respectively. The sink variable (Y) was the 7-d
average salt front location. We calculated TE for each combi-
nation of sources and sink for modeled and observed data. For
more detail on the calculation of TE please see Supporting
Information Material.
Functional performance is defined as:
Functional performanceXj !Y ¼ TEXj !Y modeled
TEXj !Y observed ,
ð3Þ
where functional performance values were calculated for
each model, and for each individual Xj
> Y relationship.

Gorski et al.
A functional performance equal to 0 is ideal, meaning that the
modeled salt front location (Y) has the same relationship to
the input (Xj ) as measured in the observed data. A functional
performance > 0 indicates that the relationship is over-
deterministic, while a functional performance < 0 indicates
over-randomness.
ML model feature importance and EGs
To assess the importance of each input feature to the
accuracy of the predictions, we use permutation feature
importance in which a feature is independently replaced
with a random sampling of values within the observed
range of that feature’s values and the trained model is used
to make predictions. The resulting error, measured as RMSE,
is compared to the error obtained using the observed
unpermuted data, and the process is repeated for each input
feature. This results in an estimate of the mean decrease in
the performance metric resulting from information loss for
each permuted feature, where larger decreases indicate
that the model relies more on that feature to improve
predictions.
EGs are a model agnostic method for calculating a
model’s local sensitivity to input variables at each individ-
ual time step of the model output. High positive or negative
EG values indicate that the input variable strongly influ-
ences the model prediction at that time step, while EG
values near zero indicate that the variable has little influ-
ence on the output. The method calculates the accumulated
gradients of the change in an output with regards to a
change in the input, df(x)/dx, as the input variable goes
from some baseline value x0 to its true value x, that is,
γ ðαÞ ¼ x0 þ αðx
x0 Þ where α = 0 at the baseline and α = 1 at the
true value of x and γ is a function describing the relationship
between x and x0 (Jiang et al. 2022) (Supporting Information
Fig. S6). The baseline values x0 are generated by sampling from
the range of the input values in the training data, given by D.
For this study, we generated 200 random samples with
replacement. Given a baseline distribution D, the EG of the
ith input variable ðΦi Þ can be calculated as the following
expectation (Erion et al. 2021):




∂f x0i þ α xi
x0i
Φi ðf ,xÞ ¼ E xi
x0i ,x0  D,α  U ð0,1Þ, ð4Þ
∂x0i
where U ð0,1Þ is the uniform distribution between 0 and 1. We
calculate the EG for each replicate model run, differing only
by random seed, and show the average EGs across model repli-
cates for visualization purposes.
While both permutation feature importance and EGs can
help assess the influence of input features globally and locally,
respectively, neither method explicitly accounts for interac-
tion between features.
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Deep learning model of Delaware Bay
Results
ML model results
The baseline ML model reproduces the structure of the salt
front record well in both training and testing periods with
RMSEs of 1.25 RM and 2.52 RM, respectively (Fig. 2a–d). The
model shows worse performance when the salt front location
is low in the estuary (< RM 58; Fig. 2e), however, model per-
formance at this range is of lower importance to the modeling
objectives which focus on salinity intrusions in the upper
estuary, and the salt front location is not tracked below RM
54. When the salt front is high in the estuary (> RM 82), the
model matches the observations well during the training
period (Fig. 2b), but underpredicts the two major peaks in
2016 and 2019 during the testing period (Fig. 2d). However,
the model did identify these as periods of salinity intrusion,
and their relative timing is well matched. These conditions are
relatively rare, representing 6.5% of the training period and
6.1% of the testing period, however they are of significant
importance from a management perspective.
In general, the model performed best under median annual
flow conditions. For example, the best performance during
the testing set was observed in 2020 (RMSE = 1.38 RM), which
was the year with the median cumulative discharge in the
Delaware and Schuylkill Rivers during the entire modeling
period. In contrast, 2016 was the year the lowest cumulative
flow in the modeling period and showed the worst perfor-
mance (RMSE = 3.31 RM). Similarly, the model performs
worse when the salt front is either low or high in the estuary
(< 58 or > 78 RM) and performs better when the salt front is
closer to its median value (Fig. 2e).
The ML model showed NSE = 0.85 during the testing
period and NSE = 0.96 during the training period. Somewhat
worse performance was reported by Meyer et al. (2020) who
used process-based and empirical models to simulate specific
conductivity at several locations within the Delaware Bay estu-
ary. They report NSE = 0.706–0.834 for the process-based
empirical model and 0.458–0.744 for a hydrodynamic model.
The modeling scheme in that study did not include holdout
data, so comparison to the training performance is more
appropriate.
Comparison of ML and COAWST hydrodynamic model
The ML model showed consistent accuracy across all 3 yr
in the testing set for which we have model results for both
models (2016, 2018, and 2019), with the best performance in
2019 (RMSE = 2.53 RM) and worst performance in 2016
(RMSE = 3.31 RM) (Fig. 3a). In contrast to the ML model, the
COAWST model showed a wider range of accuracy, with
minimum RMSE in 2019 (2.69 RM) and maximum in 2018
(8.46 RM). The two models show very similar performance in
2016 and 2019, while the ML model outperformed COAWST
in 2018 (Fig. 3a).
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Gorski et al. Deep learning model of Delaware Bay

Fig. 2. Machine learning model results for training period (a, b) and the testing period (c, d). Panel (e) shows the testing period model results broken
down by river mile interval, with the standard deviation among 10 replicates shown with error bars.

Figure 4a,c,e shows the annual time series with observed
and modeled salt front location for both models. In 2016,
both models capture the general structure of the salt front
record but fail to capture the maximal extent of the salt
front intrusion. In 2018, the COAWST model shows a consis-
tent under prediction resulting in poor overall performance,
but shows good sensitivity, matching the higher frequency
fluctuations of the salt front record similar to the ML model
(Fig. 4c). In 2019, both models capture the rising limb of the
salt front peak similarly, but the COAWST model shows supe-
rior performance in matching the maximum salt front loca-
tion (Fig. 4e).

Fig. 3. Comparison of ML model with COAWST model for each year in the testing set (a) and for each river mile interval (b), the standard deviation
among 10 replicates for the ML model is shown with error bars.

7
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Gorski et al. Deep learning model of Delaware Bay

Fig. 4. Comparison of predictions from COAWST (orange) and ML model (blue) for the salt front location for 2016 (a, b), 2018 (c, d), and 2019 (e, f).
Predictive performance for COAWST and ML models for years during the ML testing period (b, d, f) binned by performance at different river mile inter-
vals. The standard deviation among 10 replicates for the ML model is shown with error bars.

When aggregated across all 3 yr of comparison, the ML
model outperforms the COAWST model across nearly all RM
intervals (Fig. 3b); however, much of the poor performance in
the COAWST model is driven by 2018, which was a very wet
year with higher-than-average flows. The COAWST model
shows no consistent performance across RM intervals, with
worst performance at higher RM intervals in 2018 (Fig. 4d)
and best performance in 2019 (Fig. 4f).
Comparison of functional performance
To assess functional performance of the ML model and
COAWST, we focus on the relationship between 7-d average
salt front location and discharge of the Delaware River mea-
sured at Trenton, NJ (Fig. 5a) at a time lag of 7 d, and the
Schuylkill River at Philadelphia, PA (Fig. 5b) at a time lag of
8 d. For example, the salt front location on 10 October 2018 is
the average salt front location from 03 October 2018 to
10 October 2018, and its relationship to Delaware discharge
on 03 October 2018 is assessed (02 October 2018 for Schuylkill
discharge). The time lags were chosen as they showed the
strongest correlation between discharge at the two locations
and salt front in the observational data (Supporting Informa-
tion Fig. S1) and, as such, represent important time scales of
information transfer.
The ML model results show over-random behavior (func-
tional performance < 0) for 2016 and 2018 for both Delaware
and Schuylkill discharge (Fig. 5a,b). Average functional perfor-
mance for these 2 yr of
0.062 for the Delaware and
0.065

8

Gorski et al.
Fig. 5. Functional performance for (a) the relationship between the discharge 7 d previously in the Delaware River at Trenton, NJ and the 7-d average
salt front location and (b) the discharge 8 d previously in the Schuylkill River at Philadelphia, PA and the 7-d average salt front location plotted against
predictive performance for each year (symbol) and model (color). A functional performance value of 0 indicates perfect fidelity to observed relationships.
for the Schuylkill indicate that the ML model is underutilizing
the information contained within the two discharge records
by approximately 6%. However, the functional performance
for 2019 shows near-perfect representation of the discharge-
salt front relationship for the Delaware (0.002) and the
Schuylkill (
0.004).
Averaged across all years, the COAWST model shows more
accurate functional performance (closer to zero), with mean
functional performance
0.013 and
0.009 for the Delaware
and Schuylkill, respectively (Fig. 5a,b). The ML model shows

0.049 and
0.052 for Delaware and Schuylkill, respectively.
There is no consistent relationship between the functional
performance and predictive performance (RMSE) for either
model (Fig. 5), which suggests that there is not an obvious tra-
deoff between functional and predictive accuracy. For exam-
ple, in 2018 the COAWST model shows poor predictive
performance (RMSE = 8.46 RM), yet it also shows superior
functional performance compared to the ML models. For both
ML and COAWST model, 2018 shows the least accurate func-
tional performance. 2018 was a particularly wet year with the
highest annual cumulative flow during the modeling period
in the Schuylkill, and the second highest annual total in the
Delaware, which represent conditions outside the range seen
during ML training (U. S. Geological Survey 2022).
Feature importance and EGs
The permutation feature importance (Supporting Informa-
tion Fig. S7) shows that the discharge of the Delaware and
Schuylkill Rivers are the most and second most important var-
iables, respectively, followed by the air temperature and wind
9
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Deep learning model of Delaware Bay
speed. The feature importance calculation for every input vari-
able besides the two discharge variables resulted in very small
decreases in performance (< 0.1 RMSE), indicating that the
model relies heavily on information from discharge to make
its predictions. A version of the model with only Delaware
and Schuylkill discharge as predictors showed an RMSE = 2.81
RM, compared to 2.52 RM for the full set of predictors,
suggesting that even though individually the additional fea-
tures contribute only a small amount to improve predictive
performance, together they do improve the model.
The ML model EGs for 2019 are shown in Fig. 6b–d. The
year 2019 was chosen to highlight this method as the shift
from high discharge periods (Jan–Jul) to a prolonged summer
low-flow period (Aug–Oct) showed the clearest pattern in EGs
throughout the year. The highest magnitude EGs throughout
the year are generally discharge from the Delaware and the
Schuylkill Rivers (Fig. 6b). These gradients respond to the dis-
charge record and attribute large decreases in the predicted salt
front with high discharge events. For example, the large dis-
charge event in January in the Delaware River (Fig. 6a; blue
line) results in a large magnitude negative gradient (decreased
salt front prediction) for Delaware discharge (Fig. 6b; red line).
Similarly, a large discharge event in July in the Schuylkill River
(Fig. 6a; green line) results in a large magnitude negative gradi-
ent (decreased salt front prediction) for Schuylkill discharge
(Fig. 6b; gold line).
The EGs associated with discharge peaks are generally nega-
tive, reflecting the fact that discharge values greater than base-
line generally tend to result in a decrease in the location of
the predicted salt front. Similarly, generally positive EG values
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Gorski et al. Deep learning model of Delaware Bay

Fig. 6. Salt front observations and ML predictions plotted with discharge from the Delaware River at Trenton and the Schuylkill River for 2019 (a). Daily
expected gradients for model predictor variables (b–d).

for discharge during the summer months and other low-flow predicted salt front to below baseline low-flow conditions.
periods show that the model is attributing an increase in the Near the end of the summer low-flow period, EGs show the

10

Gorski et al.
model is attributing a decrease in the predicted salt front to an
increase in discharge, such as the Delaware discharge in
October and November that push the salt front downstream
from its annual maximum. Supporting Information Fig. S6
shows a schematic representation of the how the EGs are
accumulated during discharge events and low-flow periods.
During the summer low-flow period, when there are fewer
discharge events, the magnitudes of the discharge EGs are
smaller than other parts of the year. During this period, the
water level residuals (Fig. 6c), and the wind direction EGs
(Fig. 6d) show greater magnitude, indicating that the model is
relying more heavily on tidal and meteorological input data
during periods of low discharge.
Discussion
Spatial variability in modeling results
The ML models showed consistent spatial variability in
model predictive performance (Figs. 2e, 4b,d,f), with generally
better performance when the salt front was in the intervals
58–78 RM, and worse above or below this range. This is likely
a result of two factors: first, during the training and testing
period, 85% and 87% of the observations of the salt front
location fall in the interval 58–82 RM, respectively. This
results in fewer opportunities for the model to learn the
dynamics of the more extreme values, leading the model to
make predictions that are biased toward central values. Simi-
larly, during the training period, the maximum salt front loca-
tion was RM 89, while during the testing period, there were
13 d in which the salt front exceeded that value, indicating
that the testing period represented an extrapolation into
unseen conditions. These observations are consistent with
other studies that have shown ML models (Frame et al. 2022;
Kayalvizhi et al. 2022) and other modeling approaches
(Brunner et al. 2021) can struggle to match extreme values
even if they are seen during the training period.
The second factor that contributes to the spatial variability
in model response is the physical dimensions of the estuary.
The model performance was assessed separately in RM inter-
vals using geographic and bathymetric control points. Hydro-
dynamic studies of the Delaware Bay estuary show that
bathymetric control points can exert significant control on
salinity dynamics (Cook et al. 2023).
RM 58 is the location of the Chesapeake and Delaware
Canal, connecting the Chesapeake and Delaware Bays. Below
this point, the estuary opens into the Delaware Bay where
salinity dynamics are governed by tidal energy and belong to
a distinct regime from the upper estuary. Any salt front loca-
tions below RM 54 were removed from the input data, but
observations between 54 and 58 were retained to provide a
softer lower limit for the model. The ML model generally
over-predicts the salt front location over this interval,
resulting in an RMSE = 3.84 RM (Fig. 2e). Some of the error in
this region is likely due to the influence of the canal, which
11
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Deep learning model of Delaware Bay
can have bi-directional flow throughout the year (Wong 2002)
and was not included as input in either model.
Upstream of RM 58, the river tapers in width from  5 km
at RM 58 to 2.8 km at RM 68. The interval from RM 68 to
70 represents a narrowing of the river below the mouth of
Christina River, which drains the urban and suburban areas
surrounding Wilmington, DE. From RM 70 to 78, the river has
a narrow, deep central channel. The model shows the best
performance over these three intervals (RMSE = 1.92 RM for
58–68; RMSE = 1.68 RM for 68–70; and RMSE = 2.97 RM for
70–78).
Between RM 78 and 82, the deep central channel of the
river widens, allowing for more lateral transport and mixing,
leading to a more complex relationship between discharge
and salt front location and likely also influencing performance
(RMSE = 3.83 RM). Above RM 82 the river approaches the
urban and suburban areas surrounding Philadelphia, PA and is
influenced by discharge from Chester Creek and the Schuylkill
River (RMSE = 3.86 RM). These intervals are more strongly
influenced by urban runoff, which may complicate salinity
dynamics further (Sharp et al. 2009). In addition, these areas
contain groundwater wells that are used for drinking water
abstraction from the underlying Potomac-Raritan-Magothy
formation. Pumping in these wells can induce recharge from
the river into the groundwater system, which represents an
additional factor not accounted for by this modeling frame-
work (Navoy et al. 2005).
How well is the ML model representing the physical
system?
Consistent with other studies of salinity dynamics in the
Delaware Bay, the ML model identified discharge in the main
stem of the Delaware River as the most important driver of
the salt front, followed by discharge in the Schuylkill River
(Supporting Information Fig. S7) (Wong 1995; Sharp
et al. 2009; Ross et al. 2015). Further analysis of the relation-
ship between discharge and salt front indicate that the ML
model is underutilizing the information contained within the
two discharge inputs (Fig. 5a,b) during 2016 and 2018, while
the functional performance for 2019 was near-perfect. These
results suggest that under “normal” conditions, like 2019, the
ML model does as well as the COAWST model in representing
the functional relationship between discharge and salt front
location.
In 2016 and 2018, COAWST shows better functional per-
formance than the ML model. This result is not surprising, as
the hydrodynamic model forces physically realistic flow at
every time step. Even so, the EGs and feature importance
together show that the ML model identified the most impor-
tant drivers in the system and developed physically realistic
relationships between inputs and outputs. Furthermore, it
showed that those relationships could be used to predict the
salt front location under a wide range of conditions, as 2016
had the lowest combined discharge (Delaware plus Schuylkill)

Gorski et al.
of any year in the modeling period. As noted, 2016 and 2018
represent low and high discharge end members in the model-
ing set, respectively, while 2019 represents a more typical dis-
charge year in both the Delaware and Schuylkill Rivers.
The decreased functional performance in 2016 and 2018
may be a result of several factors. First, average conditions are
better represented in the training set and therefore more accu-
rately simulated in the testing set, similar to predictive perfor-
mance results. In addition, the seven- and eight-day time lags
used to assess functional performance from Delaware and
Schuylkill discharge, respectively, represent the average maxi-
mum magnitude correlation between discharge and salt
front location throughout the entire modeling time period.
However, viewed on an annual basis, the time lag of the
maximum magnitude correlation varies as a function of
the cumulative discharge amount (Supporting Information
Fig. S8). This serves to highlight the year-to-year variability in
the duration and strength of system memory that is disrupted
by frequent discharge events (i.e., 2018) and extended by pro-
longed periods of low-flow (i.e., 2016). In general, drier years
show longer time lags of maximum association between dis-
charge and salt front location indicating longer system mem-
ory under drier conditions. As such, the assessment of
functional performance at the time lag of maximum magni-
tude correlation may be most relevant for median flow years,
while greater (lesser) time lags are likely more important for
drier (wetter) years. Similar relationships have been noted in
others estuary systems, for example, Qiu and Wan (2013)
defined a piece-wise autoregressive relationship between dis-
charge and salinity dynamics for different discharge regimes
in the Caloosahatchee River Estuary.
While LSTMs are temporally aware ML algorithms and
would ideally identify these patterns directly from the data, a
process guided deep learning approach might be particularly
useful in such a setting where critical time scales are variable
and knowable (Read et al. 2019). To improve model functional
performance at a particular time lag, the functional perfor-
mance calculation could be incorporated into the ML model
loss function. However, care must be taken to ensure that
there is independent assessment of functional performance
and that the modeling approach is not subject to kludging,
where the model is tuned to fit an overly narrow set of perfor-
mance metrics (Clark 1987; Ruddell et al. 2019).
In addition, the modeling target variable is calculated
from observations. The interpolation naturally introduces
uncertainty into the exact location of the salt front. This
uncertainty could be reduced by predicting salinity at a spe-
cific location or several locations where observational data
are available.
Leveraging the strengths of hydrodynamic and ML models
together
The ML model presented in this study can be trained and
used to make 20 years of predictions in a wall time of
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Deep learning model of Delaware Bay
approximately 20 min on 16 2.60 GHz processors, while the
COAWST model runs in approximately 50 h on 180 processors
to produce a single year of predictions (4000 CPU hours per
year). As noted previously, the COAWST model produces 2 TB
of model output, with high-resolution estimates of water level,
temperature, salinity, and other variables. For detailed investi-
gations of estuarine circulation, the information gained is
often worth additional computational cost. However, for pre-
diction tasks such as the location of the salt front, or water
quality constituent concentrations at various discrete loca-
tions, a ML approach such as the one shown here can produce
similarly accurate results at a fraction of the computational
cost. This has significant implications for the ability of such a
model to help inform management decisions. The relative
speed and flexibility of the ML approach means that the
model could be altered or improved more easily based on
stakeholder suggestions. For example, in its current form the
ML model could be adjusted to make predictions of salinity at
several specific locations throughout the estuary, assuming
that the training data at those locations were obtainable. In
addition, the ML models can be used to run a wider suite of
scenarios that might cover potential future climate conditions
and management actions than what would be feasible using a
hydrodynamic model.
Similar advantages have been noted in several other diverse
estuarine systems. For example, in the Chesapeake Bay, salin-
ity and temperature response to climate change scenarios were
modeled using statistical trees, a data-driven technique similar
to traditional tree-based ML methods (Muhling et al. 2018). In
addition, estuary systems along the Gulf of Mexico USA, the
Pearl River in China, and the Danshui River in Taiwan have
been successfully modeled using ML approaches with applica-
tions to forecasting and operational early warning systems
(Chen et al. 2016; Zhou et al. 2021; Weng et al. 2024). In the
Caloosahatche River Estuary in Florida, USA a statistical model
was competitive with a three-dimensional hydrodynamic
model and the statistical model was shown to be particularly
useful for forecasting in support of upstream water resource
decision-making (Qiu and Wan 2013).
Investigating the coupling of the ML model to upstream
reservoir operations models to quickly run scenarios could
reveal how different timing and magnitude of reservoir
releases affect the movement of the salt front. Such informa-
tion could have direct application to reservoir operation and
water resource management and relies heavily on the rigorous
model evaluation conducted in the current study to demon-
strate the predictive and functional accuracy of the ML model-
ing approach.
Despite the clear computational advantages, the direct
comparison of the ML models with COAWST showed that
there were conditions in which the hydrodynamic model con-
sistently outperformed the ML model. For example, the maxi-
mum salinity intrusion in 2019 was much better matched by
COAWST than the ML model (Fig. 4e). As such, the ML model

Gorski et al.
should not be used in its current form to make predictions of
the extent of salinity intrusion during extreme events when
the salt front is ≥  82 RM. This highlights the utility of a dual
modeling approach, where process-based models can be used
in conjunction with ML approaches to collectively improve
the performance and extrapolative power of each approach.
While we focus on a comparison of modeling approaches in
this study, future work could be focused on conceptual and/or
computational integration of the models, for example through
alteration of the ML loss function to conserve mass in the sys-
tem (Read et al. 2019), using a ML model to emulate COAWST
output (Chen et al. 2018), or rewriting portions of the
COAWST model in a differentiable language to employ a dif-
ferentiable ML framework (Feng et al. 2022). Further, the cur-
rent model could be improved by including additional
observational or modeled input data to drive the model. For
example, records of discharge and/or salinity from contribut-
ing tributaries could increase model performance. In addition,
the incorporation of more historical data that represents
extreme conditions may help to increase the model perfor-
mance, particularly at the model extremes. For example, the
records of discharge and salt front are available for
the drought of record for the area in the 1960s and could be
included in future training runs; however, complete meteoro-
logical observations are sparser historically, such that tradeoffs
might include the need to interpolate input data and/or
employ a simpler ML model.
Conclusions
In this study, we developed a ML model to make hindcast
predictions of the 7-d average 250 mg L
1 isochlor in the
Delaware Bay estuary over the period 2001–2020. In compari-
son to results from a state-of-the art hydrodynamic model, the
ML model produces overall more accurate results and similarly
accurate functional coupling between inputs and outputs at a
drastically reduced computational cost. The EGs of the ML
model reveal that it has learned physically reasonable relation-
ships, and the model is able to make accurate predictions
under a wide range of conditions. While there are areas of
potential improvement (e.g., prediction of extreme values,
quantification of uncertainty), the current approach already
shows promise for flexible exploratory and predictive model-
ing of estuary salinity dynamics in support of management
decisions.
Data availability statement
All data and code used in modeling is available at https://
doi.org/10.5066/P9IK5Y45.
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Conflict of Interest
Sci. 263: 107628. doi:10.1016/j.ecss.2021.107628
The authors declare no conflicts of interest.
Acknowledgments
GG, SC, AS, AA, TT, JS, and ST were funded by the USGS Water Avail- Submitted 27 January 2023
ability and Use Science Program. SC and JW were additionally funded by Revised 05 September 2023
USGS Coastal and Marine Hazards and Resources Program. The authors Accepted 06 March 2024
would like to thank Amy Shallcross and the staff of the Delaware River
Basin Commission for thoughtful insight and productive discussion Deputy Editor: Julia C. Mullarney

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