SanJuan Benthic FINAL

San Juan Harbor Mitigation Sand Source, San Juan, Puerto Rico
Benthic Resource Survey
USACE Contract No. W912EP21A0006

Work Order W912EP21F0142
October 2021
Prepared for: Prepared by:
U.S. Army Corps of Engineers LG2 Environmental Solutions, Inc. CSA Ocean Sciences Inc.
Jacksonville District 10475 Fortune Parkway, Suite 201 8502 SW Kansas Avenue
701 San Marco Boulevard Jacksonville, Florida 32256 Stuart, Florida 34997
Jacksonville, Florida 32207
San Juan Harbor Mitigation Sand Source, San Juan, Puerto Rico
Benthic Resource Survey
USACE Contract No. W912EP21A0006, Work Order W912EP21F0142
DOCUMENT NO. CSA-LG2-FL-21-81695-3687-04-REP-01-VER01
Internal review process
Version Date Description Prepared by: Reviewed by: Approved by:

Initial draft for
D. Kilbane
INT-01 09/20/2021 science and tech L. Kabay D. Kilbane
D. Snyder
review
Client deliverable
Version Date Description Project Manager Approval
01 10/04/2021 Client deliverable D. Kilbane
02 11/10/2021 Final deliverable M. Howell
The electronic PDF version of this document is the Controlled Master Copy at all times. A printed copy is considered to be
uncontrolled and it is the holder’s responsibility to ensure that they have the current version. Controlled copies are available
upon request from the CSA Document Production Department.
San Juan Harbor Benthic Resource Survey
Table of Contents
Page
List of Tables .............................................................................................................................................. iv

List of Figures............................................................................................................................................. iv
List of Photos ............................................................................................................................................... v
List of Acronyms and Abbreviations ....................................................................................................... vi
1.0 Background.......................................................................................................................................... 1
2.0 Survey Methodology ........................................................................................................................... 2
2.1 SURVEY APPROACH................................................................................................................. 2
2.1.1 Preliminary Visual Reconnaissance .................................................................................... 2
2.1.2 Quantitative Transect Sampling.......................................................................................... 6
3.0 Results ................................................................................................................................................ 10
3.1 PRELIMINARY VISUAL RECONNAISSENCE ..................................................................... 10
3.1.1 Survey Areas 1A and 1B - Channel .................................................................................. 10
3.1.2 Survey Area 2 – Condado Lagoon and Marina................................................................. 13
3.2 QUANTITATIVE TRANSECTS ............................................................................................... 15
3.2.1 Survey Areas 1A and 1B – Channel ................................................................................. 15
3.2.2 Survey Area 2 – Condado Lagoon and Marina................................................................. 19
3.3 WILDLIFE OBSERVATIONS ................................................................................................... 25
3.4 SUMMARY ................................................................................................................................ 29
4.0 References .......................................................................................................................................... 31
Appendices ................................................................................................................................................. 32
Appendix A - Photographic Still Images............................................................................................ A-1
Appendix B - Field Logbook Entries ................................................................................................. B-1
Appendix C - Field Data Sheets ......................................................................................................... C-1
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List of Tables
Table Page
1 Braun-Blanquet scale (score) and percent cover scale values (Braun-Blanquet, 1932;
Fourqurean, et al., 2001)............................................................................................................ 8
2 Interpolation of Mid-Point Braun-Blanquet Scores (B-B score) to Percent Cover
Conversion Table ...................................................................................................................... 9
3 Results of quantitative sampling of hardbottom sites in Survey Areas 1A and 1B ................. 16
4 Total seagrass coverage by survey area derived from point-intercept sampling of
Survey Area 2 (Condado Lagoon and Marina) transects......................................................... 22
5 Mean Braun-Blanquet scores (B-B scores) and converted percent cover (% cover)
from regression by species, taken only from transects with seagrasses present for
38 Lagoon transects and 4 Marina transects ............................................................................ 23
6 Macroinvertebrates (organized by major phylogenetic group) observed Survey
Areas 1 and 2 during the field survey ...................................................................................... 26
7 Fishes (organized by family) observed in Survey Areas 1 and 2 during the field
survey ...................................................................................................................................... 27
List of Figures
Figure Page
1 Survey areas in the Puerto Nuevo Channel and Condado Lagoon for the USACE San
Juan Harbor Mitigation Sand Source Project, Puerto Rico ....................................................... 1
2 Towed video transects in the Puerto Nuevo Channel for the USACE San Juan Harbor
Mitigation Sand Source Project, Puerto Rico ............................................................................ 3
3 Towed video transects in Condado Lagoon for the USACE San Juan Harbor
Mitigation Sand Source Project, Puerto Rico ............................................................................ 4
4 Towed video transects from the channel (Survey Areas 1A and 1B) in relation to
delineated hardbottom polygons labeled as Sites 1, 2, 3, and 4 .............................................. 11
5 Towed video transects from Condado Lagoon showing presence of seagrasses and
sediments ................................................................................................................................. 14
6 Mapped Seagrass cover as determined from point intercepts in Condado Lagoon ................. 20
7 Mapped Seagrass cover as determined from point intercepts in the Marina ........................... 24
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San Juan Benthic Resource Survey
List of Photos
Photo Page
1 Camera system and lights mounted on an aluminum tow body ................................................ 5

2 Radio telemetry buoy with attached digital GPS antenna (archival photo) ............................... 6
3 The 1-m2 quadrat used for quantitative sampling in hardbottom and seagrass habitats ............ 7
4 Turf algae, cyanobacteria, and sponges (Haliclona sp.) observed at Site 1 of
Survey Area 1A ....................................................................................................................... 12
5 Natural eroded limestone hardbottom at Site 3 of Survey Area 1B on the northeastern
side of the channel ................................................................................................................... 12
6 Hardbottom feature characterized by mixed turf algae and a cyanobacteria film,
sponges, and a stony coral colony of Montastrea cavernosa in Survey Area 1A along
the southeastern side of the channel ........................................................................................ 13
7 Turf algae, sponges (Xestospongia muta), and other epibiota in Survey Area 1A
along the southwestern side of the channel ............................................................................. 16
8 Upright sponges (Lissodendoryx sp.) and other epibiota in Survey Area 1A along the
southwestern side of the channel ............................................................................................. 17
9 A large brain coral colony (Pseudodiploria clivosa) in Survey Area 1A along the
southwestern side of the channel ............................................................................................. 17
10 Cyanobacteria and brain coral (Pseudodiplora strigosa) in Area 1B along the
northeastern side of the channel .............................................................................................. 18
11 Cyanobacteria and sponge (Haliclona sp.) within Survey Area 1B on the northeastern
side of the channel ................................................................................................................... 18
12 A dense stand of turtle grass (Thalassia testudinum) in Condado Lagoon.............................. 21
13 A dense stand of Halophila stipulacea in Condado Lagoon ................................................... 21
14 A mixed seagrass stand with turtle grass (Thalassia testudinum) and manatee grass
(Syringodium filiforme) in Condado Lagoon........................................................................... 22
15 A mixed stand of seagrasses (Thalassia testudinum and Halophila stipulacea)
macroalgae (Halimeda sp.) in the San Juan Marina ................................................................ 25
16 An upsidedown jellyfish (Cassiopea frondosa) and reticulated sea star (Oreaster
reticulatus) among mixed macroalgae in along the northern shore of Condado
Lagoon ..................................................................................................................................... 27
17 A red lionfish (Pterois volitans) among encrusted mangrove roots along the northern
shore of Condado Lagoon ....................................................................................................... 29
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List of Acronyms and Abbreviations
B-B Braun-Blanquet
BEAMR Benthic Ecological Assessment for Marginal Reefs
cm centimeter
CFMC Caribbean Fishery Management Council
CSA CSA Ocean Sciences Inc.
DGPS differential global positioning system
ESA Endangered Species Act
LG2ES LG2 Environmental Solutions, Inc.
m2 meter squared
NMFS National Marine Fisheries Service
SAV Submerged Aquatic Vegetation
USACE U.S. Army Corps of Engineers
CSA-LG2-FL-21-81695-3687-04-REP-01-VER01 vi
1.0 Background
The U.S. Army Corps of Engineers (USACE) contracted the LG2 Environmental Solutions, Inc. (LG2ES)
Team to conduct benthic resource surveys to support the USACE San Juan Harbor Mitigation Sand Source
Project (The Project). The Project proposes to fill certain dredged holes in Condado Lagoon to create habitat
as mitigation for impacts from widening the Puerto Nuevo Channel in San Juan Harbor in 2001. Suitable
dredged material has been identified in Entrance Channel Cut-6 (Cut-6). Benthic surveys of both the Cut-6
dredge area and Condado Lagoon and marina (Figure 1) were required to identify any existing resources to
be avoided during dredging and fill placement activities within the project areas. The LG2ES Team for this
effort is composed of LG2ES and CSA Ocean Sciences Inc. (CSA).
Figure 1. Survey areas in the Puerto Nuevo Channel and Condado Lagoon for the USACE San Juan
Harbor Mitigation Sand Source Project, Puerto Rico.
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2.0 Survey Methodology

The LG2ES Team conducted a benthic resource survey from 26 August to 7 September 2021 to identify and
delineate submerged benthic resources within the project areas. The LG2ES Team employed appropriate
survey methods to meet the requirements described in the Performance Work Statement and the USACE
response to vendor questions for San Juan Harbor Mitigation Sand Source Benthic Resource Survey
(W912EP21F0142). The survey included a thorough visual reconnaissance of the designated survey areas
to accurately delineate the boundaries of benthic habitats and features including seagrasses, hardbottom,
and unconsolidated substrate. The site reconnaissance was immediately followed by detailed quantitative
sampling of benthic resources present in the delineated benthic habitats. The survey dates were within the
annual timeframe recommended by the National Marine Fisheries Service (NMFS) for seagrass surveys (1
June through 30 September).
The survey areas for the Project are shown in Figure 1 and included the following:
• Survey Area 1A (South Channel)

• Survey Area 1B (North Channel)
• Survey Area 2 (Condado Lagoon and Marina)
2.1 SURVEY APPROACH
2.1.1 Preliminary Visual Reconnaissance
Preliminary visual reconnaissance was conducted via towed video transects to determine the locations of
sensitive benthic habitats within which to conduct subsequent mapping and quantitative transect sampling
in the project survey areas (Figures 2 and 3). Video recordings were collected with a camera system
mounted on an obliquely oriented aluminum tow body (Photo 1). The camera system consisted of a Deep
Sea Power & Light Micro Sea Cam 2002 with a lighting system composed of paired Deep Sea Power &
Light Sealite Spheres. The camera system interfaced with HYPACK and a Trimble SPS 461 differential
global positioning system (DGPS) to navigate the pre-plotted transect lines and orientations. Additionally,
digital navigation logging of the position of the towed video system and a real-time display of the vessel’s
actual track along the survey transects were recorded. Navigational positions were recorded at 2-Hz
intervals along each video transect. The offset of the specific sled position, relative to the vessel’s DGPS
position, was incorporated into the navigation database.
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Figure 2. Towed video transects in the Puerto Nuevo Channel for the USACE San Juan Harbor Mitigation Sand Source Project, Puerto Rico.
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Figure 3. Towed video transects in Condado Lagoon for the USACE San Juan Harbor Mitigation Sand Source Project, Puerto Rico.
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Photo 1 Camera system and lights mounted on an aluminum tow body.
The video system was towed along pre-plotted visual reconnaissance track lines (transects) while benthic
habitat resource specialists watched the video in real-time recording the location of any seagrass or
hardbottom habitat encountered. When the survey team encountered sensitive habitats, they communicated
with the surveyor to record the start and stop points and habitat type along each reconnaissance transect.
Subsequent in-situ quantitative transect sampling was conducted only where submerged aquatic vegetation
(SAV) and hardbottom habitatwas identified during these reconnaissance tows. When SAV or hardbottom
habitats were identified, direct assessment by divers was implemented if needed to better understand the
nature and extent of the habitat and to establish areas for quantitative sampling. During these assessments,
divers would tow a telemetry buoy (Photo 2) which could be tracked by the HYPACK software on the
survey vessel to help define and map edgesof any identified features.
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Photo 2. Radio telemetry buoy with attached digital GPS antenna (archival photo).
2.1.2 Quantitative Transect Sampling
Based upon the results of the preliminary visual reconnaissance survey, quantitative survey transects were
assigned to any hardbottom or seagrass habitats. These modified belt-transects were 50-meters (m) long
with five randomly placed quadrats in hardbottom habitats and 100-m long with 10 randomly placed
quadrats in seagrass habitats. Transects were named according to the survey area (with prefix C=Channel,
L=Lagoon,M=Marina). For example, quantitative transects sampled in Survey Area 1, which encompasses
the channel,were designated C1, C2, etc. Hardbottom transect locations were not known prior to the field
survey anddepended on preliminary visual assessment to guide their deployment. Seagrass transects in
Condado Lagoon (but not the Marina) were pre-plotted prior to the field survey. Detailed differences in
how the transects (and quadrats) were sampled for hardbottom and seagrass habitats, respectively, are
discussed below.
Quadrat Sampling – Hardbottom Habitat

Modified belt-transects were sampled by the dive team equipped with 1-meter[s] squared (m2) quadrats
divided into 10-centimeter (cm) × 10-cm sub-cells to quantitatively assess benthic coverage within the
hardbottom habitats delineated during the preliminary visual reconnaissance survey (Photo 3).
Transects were placed randomly in identified hardbottom sites. Pre-determined random quadrat
locations were surveyed along each transect until the habitat stopped, limited visibility, or the channel
margin was reached. Benthic coverage data were collected along modified belt-transects using the
quadrat-based Benthic Ecological Assessment for Marginal Reefs (BEAMR) method (Makowski et al,
2009). Scientific divers experienced in hardbottom habitat characterization recorded maximum
hardbottom relief, sediment depth, and percent cover of sessile benthos within each quadrat. Maximum
hardbottom relief (to the nearest 0.5 cm) was measured from the lowest to highest points within each
quadrat. Sediment depth (to the nearest 0.1 cm) was measured at three random
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locations within each quadrat to determine the maximum and average sediment depth. Percent cover of
major functional sessile benthos groups was visually estimated. Each functional group (bare hard substrate,
sediment, macroalgae, turf algae, cyanobacteria, crustose coralline algae, seagrass, sponge [bioeroding
species (e.g., Clionidae) vs. nonbioeroding species], hydroid, octocoral, stony coral, anemone, zoanthid,
wormrock, sessile annelid, bivalve, bryozoan, barnacle, tunicate, and Millepora sp.) was assigned a percent
cover value from 0 to 100 percent (%); a minimum of 1% cover was given for any functional group present,
and the total percent cover of all functional groups within a quadrat added up to 100%. Biota were
identified to the lowest practical level in the field and sediment type (sand, shell-hash, and/or mud)
present in each quadrat was also noted. The percent cover of all dominant macroalgae (species/genera
with greater than 5% cover) observed were identified and macroalgal percent cover data were pooled at the
genus level. Octocorals were identified to the genus level and the maximum height was recorded to the
nearest 0.1 cm. Stony corals were identified to species and the maximum width of each colony was
recorded to the nearest 0.1 cm. Representative photographs were collected of each quadrat to supplement
the BEAMR data collection along each transect.
Photo 3. The 1-m2 quadrat used for quantitative sampling in hardbottom and seagrass habitats. The
strings demarcating the 10 × 10-cm cells are faintly visible.
Quantitative transects sampled for seagrasses were 100-m long and sampled using line intercepts and 1.0-m2
quadrats. Unlike the hardbottom transects discussed above which were not plotted ahead of time, a set of
seagrass transects were pre-plotted for Condado Lagoon prior to the field survey in anticipation of extensive
seagrass coverage around the lagoon’s periphery. To adequately cover the 28-hectare (ha) lagoon and
provide a basis for mapping seagrasses, quantitative transects were spaced systematically every 50
m. Transects were oriented approximately north to south and were positioned perpendicular to the shore.
The LG2ES Team used buoys to mark the beginning (shoreward side) and end of each survey transect
deployed from the survey vessel based on HYPACK navigation. Buoys provided visual points of
reference for the divers when laying out each quantitative transect. Quantitative transects were not pre-
plotted for seagrass habitat in the Marina area, so these were established by the field team after the visual
reconnaissance survey.
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Line Intercept Sampling

The line intercept method was used to delineate seagrass extent along each quantitative transect. Survey
data logging for each transect began on the shoreward side and continued towards the channel margin.
Scientific divers recorded the distances along each transect where seagrass/hardbottom cover started and
stopped; divers also made visual estimates of relative coverage (i.e., sparse, dense), and seagrass species
composition. The divers also qualitatively estimated the width (in meters) as far as seagrass could be
observed to each side of the diver (approximately 1.5 meters based on underwater visibility) oriented
perpendicular to each transect.
Quadrat Sampling – Seagrass Habitat

In addition to line intercepts, the transects were also sampled by the dive team equipped with 1-m2 quadrats
divided into 10-cm × 10-cm sub-cells to quantitatively assess the seagrass community (Photo 3). Pre-plotted
random quadrat locations were surveyed along each transect until seagrass stopped due to increasing water
depth, limited visibility, or the channel margin was reached. Scientific divers assessed average cover
abundance (Braun-Blanquet) and seagrass species composition as well as the number of quadrat sub-units
(cells) containing seagrass (cell count), along the survey transects. The divers also conducted density (short
shoot) counts from multiple randomly selected sub-cells within each quadrat.
Percent cover for each seagrass species, total macroalgae and, (combined) seagrass within the entire
1-m2 quadrat was recorded using the Braun-Blanquet (B-B) cover-abundance scale (Braun-Blanquet, 1932;
Fourqurean et al., 2001) shown in Table 1. The average B-B scores were then converted to percent cover
for each area to allow interpolation of averaged B-B scores that fell between B-B scale values (Table 2;
conversion was conducted by regressing the mid-point of percent cover represented within each B-B
category on the associated B-B value: Percent Cover = 2.8108*[B-B]2.2325). These percent cover scores
represent the status of seagrasses within the survey area boundaries where seagrasses occupied the seafloor.
Table 1. Braun-Blanquet scale (score) and percent cover scale values (Braun-Blanquet, 1932;
Fourqurean, et al., 2001).
Braun-Blanquet Scale Value (Score) Percent Cover (%)
0.0 Not present
0.1 Solitary specimen
0.5 Few with small cover
1 Numerous, but <5
2 5–25
3 25–50
4 50–75
5 75–100
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Table 2. Interpolation of Mid-Point Braun-Blanquet Scores (B-B score) to Percent Cover Conversion
Table.
B-B Score Percent Cover (%) B-B Score Percent Cover (%)
0.00 0.00 2.60 23.73
0.10 0.02 2.70 25.81
0.20 0.08 2.80 28.00
0.30 0.19 2.90 30.28
0.40 0.36 3.00 32.66
0.50 0.60 3.10 35.14
0.60 0.90 3.20 37.72
0.70 1.27 3.30 40.40
0.80 1.71 3.40 43.19
0.90 2.22 3.50 46.07
1.00 2.81 3.60 49.07
1.10 3.48 3.70 52.16
1.20 4.22 3.80 55.36
1.30 5.05 3.90 58.67
1.40 5.96 4.00 62.08
1.50 6.95 4.10 65.59
1.60 8.03 4.20 69.22
1.70 9.19 4.30 72.95
1.80 10.44 4.40 76.80
1.90 11.78 4.50 80.75
2.00 13.21 4.60 84.81
2.10 14.73 4.70 88.98
2.20 16.34 4.80 93.26
2.30 18.05 4.90 97.65
2.40 19.85 5.00 100.00
2.50 21.74
Endangered Species Act Listed Species and Wildlife Observations

Species of special concern including Endangered Species Act (ESA)-listed corals, seagrasses, dolphins,
manatee, and sea turtles as well as incidental fish and macroinvertebrate sightings were recorded as
observed during the benthic assessment survey. Underwater photographs were collected to adequately
represent habitats observed during the survey.
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3.0 Results
3.1 PRELIMINARY VISUAL RECONNAISSENCE
During the preliminary visual reconnaissance survey, towed video was reviewed in real-time along pre-
plotted survey lines (transects) covering a distance 15.5 kilometers (km) to identify hardbottom and
seagrasses within Survey Areas 1 (A and B) and 2.
3.1.1 Survey Areas 1A and 1B - Channel
Towed video revealed hardbottom features on both sides of the navigation channel. On the southwestern
side of the channel (Survey Area 1A), three broad hardbottom sites (Sites 1, 2, and 3) were identified during
towed video transect data collection (Figure 4). Because poor visibility hindered precise delineation of
features with the towed camera system, divers visually surveyed these broader features to assess the
hardbottom substrate and epibiota. Results of the preliminary assessment of hardbottom indicated that
quantitative transects would be sampled in Sites 2 and 4 of Survey Areas 1A and 1B, respectively.
The largest hardbottom site (Site 1) in Survey Area 1A was adjacent to the channel about mid-way along
the north-south axis and at the eastern side of the survey grid (Figure 4). Hardbottom features at this site
were boulders, rocks and rubble likely produced by past channel widening projects. Other debris such as
pipelines and cables were also present throughout the area. Hardbottom at this site was covered primarily
by cyanobacteria and sponges with no stony corals present (Photo 4).
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Figure 4. Towed video transects from the channel (Survey Areas 1A and 1B) in relation to delineated hardbottom polygons labeled as Sites 1, 2,
3, and 4.
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Photo 4. Turf algae, cyanobacteria, and sponges (Haliclona sp.) observed at Site 1 of Survey Area 1A.
A second hardbottom site (Site 2) at the northern portion of Survey Area 1A was a natural eroded limestone
feature with considerable rugosity and structural heterogeneity (Figure 4; Photo 5). This feature supported
macroalgae, sponges, stony corals and reef fishes. The third site (Site 3) was very similar in composition
to Site 2 with side-cast boulders over natural hardbottom colonized primarily by cyanobacteria with no
stony corals observed.
Photo 5. Natural eroded limestone hardbottom at Site 2 of Survey Area 1A on the northeastern side of the
channel. Fishes in the image are Spanish grunt (Haemulon macrostomum), French grunt
(Haemulon flavolineatum), reef croaker (Odontoscion dentex), porkfish (Anisotremus
virginicus), and bluehead wrasse (Thalassoma bifasciatum).
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Video transects at Survey Area 1B ran roughly perpendicular to a scarp where water depth dropped abruptly
from about 6 to 10 m (Figure 4). Boulders and other hardbottom were found along the shallow margin of
this feature. An area at the northern portion of the scarp with highest relief and evidence of epibiota
development including presence of stony coral colonies was designated Site 4. Divers reconnoitered this
area to confirm the video observations of stony corals and other epibiota (Photo 6).
Photo 6. Hardbottom feature characterized by mixed turf algae and a cyanobacteria film, sponges, and a
stony coral colony of Montastrea cavernosa in Survey Area 1B along the southeastern side
of the channel.
3.1.2 Survey Area 2 – Condado Lagoon and Marina
Seagrass presence (or absence) was documented along towed video transects in Condado Lagoon. The
general pattern observed is shown in Figure 5. Seagrasses were not observed within the deepest (>8 m)
depressions in the eastern central portion of Condado Lagoon and the area was characterized by poor
visibility and a homogeneous mud bottom. The absence of seagrasses in this area is likely due to flocculent
muds suspended in the water column preventing adequate light penetration for seagrass growth. In areas
too shallow for the survey vessel to operate safely, presence or absence of seagrasses was verified visually
from the vessel. The towed video results confirmed that seagrasses were prevalent around the periphery of
most of the lagoon and generally restricted to water depths ≤6 m. These results confirmed that the pre-
plotted, 100-m transects arranged systematically around the lagoon would be the best approach to map
seagrass cover over the entire survey area.
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Figure 5. Towed video transects from Condado Lagoon showing presence of seagrasses and sediments.
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3.2 QUANTITATIVE TRANSECTS
Quantitative transects on hardbottom habitat were sampled in Survey Areas 1A (Site 2) and 1B (Site 4). In
Survey Area 1A, on the southwestern side of the channel, three 50-m transects were sampled in Site 2
whereas two 50-m transects were sampled in Site 4 (described in Section 3.1.1). Transects were randomly
placed within hardbottom strata using random compass headings and swimming kicks to determine start
points. Each transect was sampled with 5 randomly placed 1-m quadrats.
In Condado Lagoon, divers quantitatively surveyed 11,400 m2 of the bottom with 38, 100-m transects. The
diver survey area was calculated by the linear distance the divers surveyed across each transect times a
conservative minimum field of view of 1.5 m to either side of the transect, or a total of 3.0 m. Overall, the
total coverage of seagrass was 163,234 m2. The resultant seagrass areas depicted by shaded polygons in the
maps were generated by combining data collected during the reconnaissance surveys and line intercept
sampling.
3.2.1 Survey Areas 1A and 1B – Channel
On the southwestern side of the channel (Survey Area 1A, Site 2) turf algae contributed most (37.7%) to
the biotic cover recorded along three transects (Table 3). The turf algae consisted primarily of red and brown
algae. Other biotic groups, in order of decreasing percent cover, included macroalgae, hydroids,
cyanobacteria, crustose coralline algae, sponges (boring and non-boring), bivalves, stony corals, bryozoans,
and sessile annelids. An example of the epibiota at this site is provided in (Photo 7). Macroalgae included
of Dictyota sp., Amphiroa sp, and several unidentified taxa. Sponges were represented mostly by Niphates
sp., Lissodendoryx,sp. and Haliclonia sp., but several other unidentified sponge taxa were also present
(Photo 8). Stony corals sampled in quadrats were small (1 to 14 cm) and included P. strigosa and S.
siderea. Other stony coral species including Stephanocoenia intersepta and Montastrea cavernosa were
observed in the area but not along the survey transects. Larger (20 to 50 cm) colonies of P. strigosa
and P. clivosa were sparsely distributed throughout the area and occurred in broad, flat growth forms
typical of wave-swept environments (Photo 9). No ESA-listed corals were observed within or outside the
survey transects.
Results of quantitative transect sampling in Survey Area 1B (Site 4) hardbottom provided in Table
3 indicate cyanobacteria as the predominant biotic cover in this area (67.0%). The filamentous
cyanobacteria which trapped fine sediment formed a mat-like cover of much of the hardbottom (Photo
10). Sponges, and bivalves contributed most to cover by other organisms (Photo 11). Stony corals (0.5%
cover) represented in the quadrats were small (2 to 13 cm) and occurred in 5 of 10 randomly placed
quadrats. Colonies of Pseudodiploria strigosa, P. clivosa, Montastrea cavernosa, and Siderastrea
siderea were observed in the area but outside the transect boundaries. Long-spined sea urchins
(Diadema antillarum), pencil urchins (Eucidaris tribuloides), and spiny lobsters (Panulirus argus) were
the most prevalent motile invertebrates observed along and a djacent to the transects.
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Table 3. Results of quantitative sampling of hardbottom sites in Survey Areas 1A and 1B. Two transects(10
quadrats) were sampled in Survey Area 1A and three transects (15 quadrats) were sampledin
Survey Area 1B.
Area 1A (Site 2) Area 1 B (Site 4)
Bivalve 1.7 3.0
Boring Sponge 1.6 3.0
Bryozoa 1.0 0.0
Crustose coralline algae 4.9 0.0
Hydroid 7.3 0.4
Macroalgae 8.9 0.0
Biota
Sessile Annelid 0.9 0.5
Sponge 2.4 2.1
Stony coral 1.3 0.5
Tunicate 1.0 0.3
Turf Algae 37.7 0.0
Cyanobacteria 5.3 67.0
Bare Hardbottom 10.0 0.0
Rubble 7.8 9.7
Substrate
Sand 18.9 90.0
Sediment on HB 24.1 21.1
Mean Relief (cm) 25.6 30.6
Mean Sediment Depth (cm) 1.2 2.6
Total transects 3 2
Photo 7. Turf algae, sponges (Xestospongia muta), and other epibiota in Survey Area 1A along the
southwestern side of the channel.
CSA-LG2-FL-21-81695-3687-04-REP-01-VER01 16
Photo 8. Upright sponges (Lissodendoryx sp.) and other epibiota in Survey Area 1A along the
southwestern side of the channel.
Photo 9. A large brain coral colony (Pseudodiploria clivosa) in Survey Area 1A along the southwestern
side of the channel.
CSA-LG2-FL-21-81695-3687-04-REP-01-VER01 17
Photo 10. Cyanobacteria and brain coral (Pseudodiplora strigosa) in Area 1B along the northeastern side
of the channel.
Photo 11. Cyanobacteria and sponge (Haliclona sp.) within Survey Area 1B on the northeastern side of
the channel.
CSA-LG2-FL-21-81695-3687-04-REP-01-VER01 18
3.2.2 Survey Area 2 – Condado Lagoon and Marina
Five seagrass species were recorded along the 38 transects during point-intercept data collection: Halophila
decipiens, H. stipulacea, Halodule wrightii, Thalassia testudinum, and Syringodium filiforme. A total of
163,234.2m2 of seagrasses was mapped in the 38 transects (Figure 6). T. testudinum (46,221.5 m2) followed
by H. decipiens (39,460.2 m2), and H. stipulacea (37,353.6 m2) accounted for the highest cover values
(Table 4; Photos 12 and 13). S. filiforme and H. wrightii were less abundant and usually found in mixed
associations with T. testudinum (Photo 14). Mixed associations of several species were identified from the
transect samples, the most prevalent are listed in Table 4.
CSA-LG2-FL-21-81695-3687-04-REP-01-VER01 19
Figure 6. Mapped Seagrass cover as determined from point intercepts in Condado Lagoon.
CSA-LG2-FL-21-81695-3687-04-REP-01-VER01 20
Photo 12. A dense stand of turtle grass (Thalassia testudinum) in Condado Lagoon.
Photo 13. A dense stand of Halophila stipulacea in Condado Lagoon.
CSA-LG2-FL-21-81695-3687-04-REP-01-VER01 21
Photo 14. A mixed seagrass stand with turtle grass (Thalassia testudinum) and manatee grass
(Syringodium filiforme) in Condado Lagoon.
Table 4. Total seagrass coverage by survey area derived from point-intercept sampling of Survey Area 2
(Condado Lagoon and Marina) transects.
Seagrass Coverage (m2)
Species
Condado Lagoon Marina
Thalassia testudinum 46,221.5 4,643.6
Syringodium filiforme 897.0 0
Halophila stipulacea 37,353.7 271.7
Halopila decipiens 39,460.2 2,341.8
Halodule wrightii 682.2 127.6
All seagrass 163,234.2 9,261.2
Braun-Blanquet scores for only transects with seagrasses are presented in Table 5. The highest percent
cover for estimated for individual species in Condado Lagoon was T. testudinum (14.8%) followed by
H. stipulacea (9.2%) and S. filiforme (7.4%). H. decipiens exhibited low percent cover, but was spread
widely over the lagoon (Figure 6). H. wrightii was the least abundant (0.3% cover) and sparsely distributed.
CSA-LG2-FL-21-81695-3687-04-REP-01-VER01 22
Table 5. Mean Braun-Blanquet scores (B-B scores) and converted percent cover (% cover) from regression
by species, taken only from transects with seagrasses present for 38 Lagoon transects and 4
Marina transects.
Species (Lagoon) Frequency B-B %Cover
Thalassia testudinum 23 2.1 14.8
Halophila stipulacea 15 1.7 9.2
Syringodium filiforme 5 1.5 7.4
Macroalgae 38 1.3 4.8
Halopila decipiens 23 0.8 1.5
Halodule wrightii 6 0.4 0.3
Species (Marina) Frequency B-B %Cover
Macroalgae 4 3.1 35.0
Thalassia testudinum 3 2.1 15.4
Halopila decipiens 1 1.8 10.4
Halophila stipulacea 2 0.3 0.2
Halodule wrightii 1 0.1 0.0
Marina transects (n=4) yielded four species of seagrasses with T. testudinum and H. stipulacea dominating
the cover (Table 5). Seagrasses occurred in patches usually mixed with macroalgae such as Halimeda sp.
(Figure 7; Photo 15). Cover estimates for each species (including macroalgae) as derived from B-B scores
are given in Table 5. Macroalage was the highest contributor to cover in the Marina area followed by
T. testudinum and H.decipiens.
CSA-LG2-FL-21-81695-3687-04-REP-01-VER01 23
Figure 7. Mapped Seagrass cover as determined from point intercepts in the Marina.
CSA-LG2-FL-21-81695-3687-04-REP-01-VER01 24
Photo 15. A mixed stand of seagrasses (Thalassia testudinum and Halophila stipulacea) macroalgae
(Halimeda sp.) in the San Juan Marina.
3.3 WILDLIFE OBSERVATIONS
Wildlife observations during the benthic survey included the Antillean manatee (Trichechus manatus
manatus) a subspecies of the West Indian manatee (T. manatus), listed as threatened by the US Fish and
Wildlife Service. This species was seen in the Condado Lagoon and the Marina. Conspicuous
macroinvertebrates observed during the surveys are listed in Table 6. Invertebrate species managed by the
Caribbean Fishery Management Council (CFMC), queen conch (Strombus gigas) and spiny lobster
(Panulirus argus), were observed in Condado Lagoon and the Marina. Other invertebrates observed
included the reticulated sea star (Oreaster reticulatus), long-spined sea urchin, variegated sea urchin
(Lytechinus variegatus), pen shells (Pinna sp.), and the upside-down jellyfish (Cassiopea xamachana and
C. frondosa) (Photo 16). Additional invertebrates, mostly sessile species were discussed in Section 3.2.1.
A list of fishes recorded during the survey is presented in Table 7. A total of 59 species from 28 families
were observed collectively in Survey Areas 1 and 2. Most species were observed within the hardbottom
areas in the channel. Condado Lagoon produced 24 species including mojarras, herrings, snappers,
butterflyfishes, and angelfishes. Snappers, grunts, and parrotfishes are managed by the CFMC (CFMC,
2004). Invasive red lionfish (Pterois volitans) were observed in Condado Lagoon (Photo 17) and in the
channel (Survey Areas 1A and 1B).
CSA-LG2-FL-21-81695-3687-04-REP-01-VER01 25
Table 6. Macroinvertebrates (organized by major phylogenetic group) observed in Survey Areas 1

and 2 during the field survey.
Group Common Name Scientific Name Survey Area 1 Survey Area 2
Pink vase sponge Niphates sp. +
Yellow tube sponge Aplysina sp. +
pink sponge Haliclona sp. +
Barrel sponge Xestospongia muta +
Sponges
Stinker sponge Ircinia sp. +
Fire sponge Tedania ignis +
Sponge Lissodendoryx sp. +
Boring sponge Cliona delitrix +
Kobby brain coral Pseudodiploria clivosa +
Brain coral Pseudodiploria strigosa +
Great star coral Montastrea cavernosa +
Starlet coral Siderastrea siderea + +
Club-tip finger coral Porites porites + +
Blushing star coral Stephanocoenia intersepta +
Cnidarians
Upside-down jelly Cassiopea frondosa +
Mangrove upside-down jelly Cassiopea xamachana +
Corkscrew anemone Bartholomaea annulata + +
Burrowing anemone Ceriantheomorphe +
brasiliensis
Sun anemone Stichodactyla helianthus +
Seagrass anemone Viatrix globulifera +
Algae hydroid Thyroscyphus ramosus + +
Hydroids
Hydroid Unidentified + +
Feather duster worm Sabellastarte magnifica + +
Annelids
Social feather duster Bispira brunnea +
Murex Chicoreus sp. +
Fighting conch Strombus alatus +
Molluscs
Queen conch Lobatus (Strombus) gigas +
Pen shell Pinna sp. + +
Banded cleaner shrimp Stenopus hispidus +
Hermit crab Petrochirus diogenes +
Spiny lobster Panulirus argus + +
Decapods
Elbow crab Platylambrus sp. + +
Swimming crab Portunus sp. +
Arrow crab Stenorhynchus seticornis + +
Reticulated sea star Oreaster reticulatus +
Variegated urchin Lytechinus variegatus +
Long-spined urchin Diadema antillarum + +
Echinoderms
Rock boring urchin Echinometra lacunter +
West Indian Sea Egg Tripneustes ventricosus +
Slate-pencil urchin Eucidaris tribuloides + +
Holothurians Sea Cucumber Isostichopus badionotus +
Colonial tunicates Unidentified +
Tunicates Giant tunicate Polycarpa sp. +
Black tunicate Ascida nigra +
Total taxa 30 26
+ = present
CSA-LG2-FL-21-81695-3687-04-REP-01-VER01 26
Photo 16. An upside-down jellyfish (Cassiopea frondosa) and reticulated sea star (Oreaster reticulatus)
among mixed macroalgae in along the northern shore of Condado Lagoon.
Table 7. Fishes (organized by family) observed in Survey Areas 1 and 2 during the field survey.
Family Common Name Scientific Name Survey Area 1 Survey Area 2
Dasyatidae Southern stingray Hypanus americanus +
Muraenidae Chain moray Echidna catenata +
Atherindidae Atherinomorus stipes +
Redear sardine Harengula humeralis +
Clupeidae False pilchard Harengula jaguana +
Atlantic thread herring Opisthonema oglinum +
Holocentridae Squirrelfish Holocentrus adscensionis +
Fistulariidae Bluespotted cornetfish Fistularia tabacaria +
Scorpaenidae Red lionfish Pterois volitans + +
Serranidae Coney Epinephelus cruentatus +
Sparidae Sea bream Archosargus rhomboidalis +
Pempheridae Glassy sweeper Pempheris schomburgkii +
Sciaenidae Reef croaker Odontoscion dentex +
Bar jack Caranx ruber + +
Carangidae
Yellow jack Caranx bartholomaei + +
Mojarras Eucinostomus spp. +
Gerreidae
Yellowfin mojarra Gerres cinereus +
Porkfish Anisotremus virginicus + +
Black margate Anisotremus surinamensis +
Tomtate Haemulon aurolineatum +
Caesar grunt Haemulon carbonarium +
Haemulidae
French grunt Haemulon flavolineatum + +
Spanish grunt Haemulon macrostomum +
White grunt Haemulon plumieri +
Bluestriped grunt Haemulon sciurus +
CSA-LG2-FL-21-81695-3687-04-REP-01-VER01 27
Table 7. (Continued).
Family Common Name Scientific Name Survey Area 1 Survey Area 2
Mutton snapper Lutjanus analis +
Schoolmaster snapper Lutjanus apodus + +
Lutjanidae
Dog snapper Lutjanus jocu + +
Gray snapper Lutjanus griseus +
Sphyraenidae Great barracuda Sphyraena barracuda + +
Queen angelfish Holacanthus ciliaris + +
Pomacanthidae
French angelfish Pomacanthus paru + +
Four-eye butterflyfish Chaetodon capistratus +
Chaetodontidae Banded butterflyfish Chaetodon striatus +
Spotfin butterflyfish Chaetodon ocellatus +
Ocean surgeon Acanthurus tractus +
Acanthuridae Doctorfish Acanthurus chirurgus +
Blue tang Acanthurus coeruleus +
Dusky damselfish Stegastes adustus +
Pomacentridae Cocoa damselfish Stegastes variabilis +
Sergeant Major Abudefduf saxatilis +
Spanish hogfish Bodianus rufus +
Slippery dick Halichoeres bivittatus +
Clown wrasse Halichoeres maculipinna +
Labridae
Blackear wrasse Halichoeres poeyi +
Puddingwife Halichoeres radiatus + +
Bluehead wrasse Thalassoma bifasciatum +
Stoplight parrotfish Sparisoma viride + +
Scaridae Princess parrotfish Scarus iseri +
Redfin parrotfish Sparisoma rubripinne +
Clinidae Saddled blenny Malacoctenus triangulatus +
Blenniidae Scaly blenny Labrisomus sp. +
Goldspot goby Gnatholepis thompsoni + +
Broadstripe goby Elacatinus prochilos +
Gobiidae
Orangespotted goby Nes longus +
Hyaline goby Coryphopterus sp. + +
Bothidae Peacock flounder Bothus lunatus + +
Sharpnose puffer Canthigaster rostrata + +
Tetraodontidae
Bandtail puffer Sphoeroides spengleri +
Ostraciidae Smooth trunkfish Lactophrys triqueter +
Total Species 43 31
+=present.
CSA-LG2-FL-21-81695-3687-04-REP-01-VER01 28
Photo 17. A red lionfish (Pterois volitans) among encrusted mangrove roots along the northern shore of
Condado Lagoon.
3.4 SUMMARY
Hardbottom sites worthy of quantitative survey were identified on either side of the San Juan Harbor
Federal channel (Survey Areas 1A and 1B). Three hardbottom sites were delineated in Survey Area
1A by towed video reconnaissance. These sites comprised 19.6 ha in total, about 52% of the Survey Area
1A. Two of the sites (Sites 1 and 3) were composed of mostly side cast rocks and other debris covered
primarily by cyanobacteria and sponges with no stony corals present. The other site (Site 2) consisted of
natural, eroded limestone with considerable structural complexity. Biotic cover was dominated by turf
algae composed mostly of red (Rhodophyte) taxa. This site was assessed quantitatively with three
transects. A diverse assemblage of epibiota consisting of sponges, crustose coralline algae,
hydroids, stony corals, sessile annelids, and bryozoans was present. At least five stony coral species
were sparsely distributed throughout this site, but no ESA-listed species were observed. Long-spined
urchins and spiny lobsters were observed within and outside the transects as were various reef fishes.
In Survey Area 1B a hardbottom site (Site 4) composed of natural limestone with what appeared to
be construction-related boulders and rubble was sampled with quantitative transects. This site was at the
top of a north-south facing, scarp-like feature at the channel margin and was estimated to encompass
10,734.2 m2. The hardbottom was mostly covered with filamentous cyanobacteria which trapped fine
sediment resulting in a mat-like cover. Sponges, hydroids, and stony corals sparsely contributed to the
biotic cover of the site. Larger colonies of the stony corals P. strigosa, P. clivosa, M. cavernosa, and S.
siderea were present in the area, but no ESA listed coral species were observed. Larger motile
invertebrates such as long-spined urchins, pencil urchins, spiny lobsters were present within and adjacent
to the survey transects. Various reef fishes were also observed throughout the site.
CSA-LG2-FL-21-81695-3687-04-REP-01-VER01 29
Seagrass distribution, density, and cover were estimated in Survey Area 2 (Condado Lagoon and the Marina)
along 42 quantitative transects (38 in Condado Lagoon; 4 in the Marina). Five seagrass species were
documented in these two areas. Thalassia testudinum was the most abundant of the five species followed
by the invasive Halophila stipulacea. The overall seagrass coverage in Condado Lagoon estimated from 38
transects was 163,234.2 m2 and was predominantly observed in shallow water depths (<6 m). Contributions
to this cover by the five species observed, ranked by overall cover (non-mixed stands) were T. testudinum,
H. decipiens, H. stipulacea, S. filiforme, and H. wrightii. The Marina supports 9,261.2 m2 of seagrass,
mostly located near the southern boundary and along the seawall.
H. stipulacea was second most abundant seagrass species in Condado Lagoon and the Marina. This species
is invasive, first reported from the Caribbean (Grenada) in 2004 and reaching Puerto Rico in 2017 (Winters
et al 2020). Generally found in deeper waters than T. testudinum, H. stipulacea was present at both eastern
and western portions of the Lagoon and along the Marina quantitative transects.
Survey Areas 1 and 2 were documented to support multiple benthic resources including seagrasses, stony
corals, spiny lobsters, queen conch, and fishes (e.g., snappers, groupers, grunts, and mojarras). The
information gathered during this survey should provide a basis for the protection of these resources from
activities associated with the proposed mitigation project.
CSA-LG2-FL-21-81695-3687-04-REP-01-VER01 30
4.0 References
Braun–Blanquet, J. 1932. Plant sociology: the study of plant communities. Hafner, New York. 439 p.
Caribbean Fishery Management Council 2004. Final Environmental Impact Statement For The Generic
Essential Fish Habitat Amendment to: Spiny Lobster Fishery Management Plan Queen Conch
Fishery Management Plan Reef Fish Fishery Management Plan Coral Fishery Management Plan
For The U.S. Caribbean . Volumes I and II. San Juan, Puerto Rico
Fourqurean, J.W., A. Willsie, C.D. Rose, and L.M. Rutten. 2001. Spatial and temporal pattern in seagrass
community composition and productivity in South Florida. Marine Biology 138: 341-354.
Makowski, C. , S.E. Prekel, M. Lybolt, and R.M. Baron. 2009. The Benthic Ecological Assessment for
Marginal Reefs (BEAMR) Method. Journal of Coastal Research 25(2): 515-522.
Winters G, Beer S, Willette DA, Viana IG, Chiquillo KL, Beca-Carretero P, Villamayor B, Azcárate-
García T, Shem-Tov R, Mwabvu B, Migliore L, Rotini A, Oscar MA, Belmaker J, Gamliel I,
Alexandre A, Engelen AH, Procaccini G and Rilov G (2020) The Tropical Seagrass Halophila
stipulacea: Reviewing What We Know From Its Native and Invasive Habitats, Alongside
Identifying Knowledge Gaps. Frontiers Marine Science 7:300. doi: 10.3389/fmars.2020.00300.
CSA-LG2-FL-21-81695-3687-04-REP-01-VER01 31
Appendices
CSA-LG2ES-FL-21-81695-3687-05-REP-01-VER01 32
Appendix A
Photographic Still Images
(Provided in Electronic Format)
CSA-LG2ES-FL-21-81695-3687-05-REP-01-VER01 A-1
Appendix B
Field Logbook Entries
CSA-LG2ES-FL-21-81695-3687-05-REP-01-VER01 B-1
Appendix C
Field Data Sheets
CSA-LG2ES-FL-21-81695-3687-05-REP-01-VER01 C-1

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SanJuan Benthic FINAL

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San Juan Harbor Mitigation Sand Source, San Juan, Puerto Rico

Benthic Resource Survey

USACE Contract No. W912EP21A0006

Prepared for: Prepared by:

Internal review process

Version Date Description Prepared by: Reviewed by: Approved by:

Version Date Description Project Manager Approval

01 10/04/2021 Client deliverable D. Kilbane

02 11/10/2021 Final deliverable M. Howell

List of Tables .............................................................................................................................................. iv

1 Camera system and lights mounted on an aluminum tow body ................................................ 5

List of Acronyms and Abbreviations

2.0 Survey Methodology

• Survey Area 1A (South Channel)

2.1 SURVEY APPROACH

2.1.1 Preliminary Visual Reconnaissance

Photo 1 Camera system and lights mounted on an aluminum tow body.

2.1.2 Quantitative Transect Sampling

Quadrat Sampling – Hardbottom Habitat

Line Intercept Sampling

Quadrat Sampling – Seagrass Habitat

Endangered Species Act Listed Species and Wildlife Observations

3.1 PRELIMINARY VISUAL RECONNAISSENCE

3.1.1 Survey Areas 1A and 1B - Channel

3.1.2 Survey Area 2 – Condado Lagoon and Marina

3.2 QUANTITATIVE TRANSECTS

3.2.1 Survey Areas 1A and 1B – Channel

3.2.2 Survey Area 2 – Condado Lagoon and Marina

Photo 13. A dense stand of Halophila stipulacea in Condado Lagoon.

3.3 WILDLIFE OBSERVATIONS

Table 6. Macroinvertebrates (organized by major phylogenetic group) observed in Survey Areas 1

Photographic Still Images

(Provided in Electronic Format)

Field Logbook Entries

Field Data Sheets

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