The side scan sonar survey was done simultaneously with the bathymetry swath survey and used an EdgeTech Model 4125 Towfish bow-mounted from Lookdown at 400 and 900 kHz. The 4125 Towfish utilizes EdgeTech’s Full Spectrum CHIRP technology to produce higher resolution images than a non-CHIRP system. EdgeTech Discovery Software was used to acquire the side scan sonar data using the JSF format at a resolution of about 2.3 cm. All JSF files collected using EdgeTech’s Discover Software were processed using John Gann’s Chesapeake Technology SonarWiz5. Dimensions of contacts should be considered accurate to +/- 30% of the measured dimensions. This system also records the direct arrival intensity data.

1m depth contours, derived from Sandy Hook bayside bathymetry, 1m resolution raster. The side scan sonar survey was done simultaneously with the bathymetry swath survey and used an EdgeTech Model 4125 Towfish bow-mounted from Lookdown at 400 and 900 kHz. The 4125 Towfish utilizes EdgeTech’s Full Spectrum CHIRP technology to produce higher resolution images than a non-CHIRP system. EdgeTech Discovery Software was used to acquire the side scan sonar data using the JSF format at a resolution of about 2.3 cm. All JSF files collected using EdgeTech’s Discover Software were processed using John Gann’s Chesapeake Technology SonarWiz5. Dimensions of contacts should be considered accurate to +/- 30% of the measured dimensions. This system also records the direct arrival intensity data.

Conductivity, Temperature, and Depth (CTD) Profiles associated with submerged mapping cruises. The side scan sonar survey was done simultaneously with the bathymetry swath survey and used an EdgeTech Model 4125 Towfish bow-mounted from Lookdown at 400 and 900 kHz. The 4125 Towfish utilizes EdgeTech’s Full Spectrum CHIRP technology to produce higher resolution images than a non-CHIRP system. EdgeTech Discovery Software was used to acquire the side scan sonar data using the JSF format at a resolution of about 2.3 cm. All JSF files collected using EdgeTech’s Discover Software were processed using John Gann’s Chesapeake Technology SonarWiz5. Dimensions of contacts should be considered accurate to +/- 30% of the measured dimensions. This system also records the direct arrival intensity data.

Collection of benthic infauna and epifauna used a 0.04 m2 Ted Young Modified Van Veen grab. Three replicate benthic samples were collected at 23 sites to total 69 samples in Year 1. The samples were immediately sieved over a 0.5 mm mesh screen. The residue remaining on the screen was fixed in 3.7% formaldehyde solution in seawater, buffered with sodium borate and containing Rose Bengal to stain organisms. A fourth grab was collected for sediment analysis. Sediment for grain size analysis was wet-sieved through a 63μm-mesh sieve in distilled water with dispersant to disaggregate and separate the silt and clay fraction from the sand-sized fraction. Silt and clay mass was determined by drying a known volume of the water-particle mixture passing through the sieve. The sand fraction was dried and then sieved into the following size fractions: <63 µm (silt), 63-125 µm (very fine sand), 125-250 µm (fine sand), 250-500 µm (medium sand), 500-1000 µm (coarse sand), >1000 µm (very coarse sand). Each fraction was weighed. The mass of the <4φ fraction was further analyzed using a Spectrex model PC-2000 laser particle counter (Spectrex Corporation, Redwood City, CA) Counts of particles were obtained corresponding to these additional size categories: 5φ (4-8 µm very fine silt), and 6φ (16-31 µm, medium silt), 7φ (8-16 µm, fine silt), 8 φ ( 4-8 µm, very fine silt), and 9 φ (2-4 µm, clay). Particle counts were converted to mass by multiplying the fractional volume percent in each size category by the total mass of the <4φ fraction determined during wet sieving.

Supervised classification utilized training texels of 30 x 30 to 90 x 90 pixels cut from GeoTiff orthotiles centered on the coordinates of the grab sample stations. Each texel was assigned to a cluster training set based on that sample’s classification in the original (latent) cluster analysis calculated on similarity of sediment characteristics. However, none of the potential 2470 combinations of backscatter signal characters and their treatments were able to discriminate significantly among these 5 classes, meaning that variation among samples of at least 2 classes overlapped considerably. Recombination into 4 classes (combining Classes 3 and 4) yielded significant discrimination. Mapping of the results showed that one of these classes was likely to be legitimate when applied to the bayside, but additionally was duplicated as an artifact of edge between orthotiles on the oceanside because of fading at the swath margins. This means that backscatter was characteristic of the larger habitat distinctions shown in the latent dendrogram with confidence, and of lesser branches with less confidence. Therefore, the entire oceanside was characterized as one habitat, and classification of the bayside was attempted again in isolation. Recombination into 3 classes (“mud”, “sand”, “gravelly sand”) was able to resolve 3 classes significantly (score = 0.33548) using input factors Contrast, Gray Mean, and Directionality with 30 x 30 pixel (15 x 15 m) texels. Despite good separation in the training texels, with some slight overlap at the 5% confidence ellipsoid for mud and gravel, most areas known to be muddy were classified as being gravelly sand in the resulting classification map. This is likely a function of reflective shell hash in acoustically dark mud having similar contrast to reflective gravel with acoustically dark shadows created by high relief. A test of natural separation (Davies-Bouldin Index) indicated four modes using these characters, so the same factors were used in an unsupervised classification allowing four latent classes. The four latent classes mapped very similar to the previous supervised classification but broke up the latent analog to the “gravelly sand” class. Class error was low at 0.1110. The newly resolved class was clearly mud with shell, based on video ground truthing. This class was combined with the mud class in compiling the final habitat classification map.

The side scan sonar survey was done simultaneously with the bathymetry swath survey and used an EdgeTech Model 4125 Towfish bow-mounted from Lookdown at 400 and 900 kHz. The 4125 Towfish utilizes EdgeTech’s Full Spectrum CHIRP technology to produce higher resolution images than a non-CHIRP system. EdgeTech Discovery Software was used to acquire the side scan sonar data using the JSF format at a resolution of about 2.3 cm. All JSF files collected using EdgeTech’s Discover Software were processed using John Gann’s Chesapeake Technology SonarWiz5. Dimensions of contacts should be considered accurate to +/- 30% of the measured dimensions. This system also records the direct arrival intensity data.

Collection of benthic infauna and epifauna used a 0.04 m2 Ted Young Modified Van Veen grab. Three replicate benthic samples were collected at 23 sites to total 69 samples in Year 1. The samples were immediately sieved over a 0.5 mm mesh screen. The residue remaining on the screen was fixed in 3.7% formaldehyde solution in seawater, buffered with sodium borate and containing Rose Bengal to stain organisms. A fourth grab was collected for sediment analysis. Sediment for grain size analysis was wet-sieved through a 63μm-mesh sieve in distilled water with dispersant to disaggregate and separate the silt and clay fraction from the sand-sized fraction. Silt and clay mass was determined by drying a known volume of the water-particle mixture passing through the sieve. The sand fraction was dried and then sieved into the following size fractions: <63 µm (silt), 63-125 µm (very fine sand), 125-250 µm (fine sand), 250-500 µm (medium sand), 500-1000 µm (coarse sand), >1000 µm (very coarse sand). Each fraction was weighed. The mass of the <4φ fraction was further analyzed using a Spectrex model PC-2000 laser particle counter (Spectrex Corporation, Redwood City, CA) Counts of particles were obtained corresponding to these additional size categories: 5φ (4-8 µm very fine silt), and 6φ (16-31 µm, medium silt), 7φ (8-16 µm, fine silt), 8 φ ( 4-8 µm, very fine silt), and 9 φ (2-4 µm, clay). Particle counts were converted to mass by multiplying the fractional volume percent in each size category by the total mass of the <4φ fraction determined during wet sieving.

Polygon shapefile showing the coverage area of the acoustic mapping at Sandy Hook, NJ between July 2015 and August 2015. The side scan sonar survey was done simultaneously with the bathymetry swath survey and used an EdgeTech Model 4125 Towfish bow-mounted from Lookdown at 400 and 900 kHz. The 4125 Towfish utilizes EdgeTech’s Full Spectrum CHIRP technology to produce higher resolution images than a non-CHIRP system. EdgeTech Discovery Software was used to acquire the side scan sonar data using the JSF format at a resolution of about 2.3 cm. All JSF files collected using EdgeTech’s Discover Software were processed using John Gann’s Chesapeake Technology SonarWiz5. Dimensions of contacts should be considered accurate to +/- 30% of the measured dimensions. This system also records the direct arrival intensity data.

Collection of benthic infauna and epifauna used a 0.04 m2 Ted Young Modified Van Veen grab. Three replicate benthic samples were collected at 23 sites to total 69 samples in Year 1. The samples were immediately sieved over a 0.5 mm mesh screen. The residue remaining on the screen was fixed in 3.7% formaldehyde solution in seawater, buffered with sodium borate and containing Rose Bengal to stain organisms. A fourth grab was collected for sediment analysis. Sediment for grain size analysis was wet-sieved through a 63μm-mesh sieve in distilled water with dispersant to disaggregate and separate the silt and clay fraction from the sand-sized fraction. Silt and clay mass was determined by drying a known volume of the water-particle mixture passing through the sieve. The sand fraction was dried and then sieved into the following size fractions: <63 µm (silt), 63-125 µm (very fine sand), 125-250 µm (fine sand), 250-500 µm (medium sand), 500-1000 µm (coarse sand), >1000 µm (very coarse sand). Each fraction was weighed. The mass of the <4φ fraction was further analyzed using a Spectrex model PC-2000 laser particle counter (Spectrex Corporation, Redwood City, CA) Counts of particles were obtained corresponding to these additional size categories: 5φ (4-8 µm very fine silt), and 6φ (16-31 µm, medium silt), 7φ (8-16 µm, fine silt), 8 φ ( 4-8 µm, very fine silt), and 9 φ (2-4 µm, clay). Particle counts were converted to mass by multiplying the fractional volume percent in each size category by the total mass of the <4φ fraction determined during wet sieving.