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Nearshore Submerged

Extent Condition Protection/Restoration


Nearshore submerged habitat includes the seafloor and water column found below the low tide line extending from the mouth of coastal rivers to a depth of about 100 feet. Nearshore submerged is broken down into two sub habitats by depth: the nearshore shallow (0 to 20 feet) and the nearshore deep habitat (20 to 100 feet). The nearshore submerged habitats include a range of substrate types, the water column, large three dimensional seafloor features (e.g. ledges, banks, and basins), and live or deposited organic matter (e.g. eelgrass, macroalgae, shell hash) (Massachusetts Ocean Management Plan, 2009). The distincition between nearshore shallow and nearshore deep habitats was developed for the purposes of the Boston Harbor Habitat Atlas by the Boston Harbor Habitat Coalition.

Substrate types are categorized by sediment size into five main categories: mud, sand, gravel, cobble, and boulder (see photos below). The categories are defined according to the percent composition of sand, gravel, and mud. According to the sediment classification scheme as developed by Shephard (1954) and modified by Schlee (1973), sediments with more than 10% gravel are considered gravel or gravelly sediment and sediments with less than 10% gravel are considered sand or mud. These seafloor types may also be categorized as either soft bottom (mud, sand, gravelly sediment, or gravel) or hard bottom communities (cobble or boulder) (Callaghan, 2011).

Mud, Sand, Gravel Cobble, and Boulder Substrates categorized according to percent gravel, sand and mud (USGS)
Figure 1: Mud, sand, gravel, cobble, and boulder substrates categorized according to Shepard (1954) as modified by Schlee (1973)(USGS)

A mosaic of substrates and the various plants and animals that they support comprise the nearshore submerged habitats. Species commonly found inhabiting these areas vary depending on the substrate type. Soft bottom substrates in Boston Harbor provide habitat for infaunal species (benthic animals which live within the substrate) such as juvenile fish, quahogs and sand dollars, while hard bottom substrates provide habitat for epifaunal communities (benthic animals which live on the surface of a substrate) including crustaceans, mollusks, macroalgae, sponges, bryozoans and cnidarians. These varied species which live, build, and alter the seafloor, combined with the nature of ocean currents, river outflows, and storms, subject the nearshore submerged habitats to frequent re-suspension, transport, and relayering of seafloor sediments (Massachusetts Ocean Management Plan, 2009).

Lobster on seafloor
Figure 2: Lobster on seafloor (P. Colarusso)

The nearshore submerged habitats provide feeding, breeding and refuge habitat for a wide variety of fin and shellfish species, crustaceans, and mollusks. As such, these habitats are critical in the support of commercially and recreationally important fisheries. The shallow nearshore waters provide refuge habitat to winter flounder, smelt, menhaden silversides, sand lance, eels, herring, striped bass, and bluefish. Shallow nearshore habitat also provides a food source for diving bird species (Massachusetts Ocean Management Plan, 2009).


The nearshore submerged habitats (especially the nearshore shallow habitat) were dramatically altered as the City of Boston was settled. Areas along and near the coast were filled to expand the city and allow for coastal development, resulting in substantial losses in this important habitat. Mass DEP, along with CZM, delineated the historic mean high water line in the Boston Harbor region for purposes of understanding the regulatory jurisdiction of filled tidelands. Although the nearshore submerged habitats begin at the low tide line, this project gives an understanding of the magnitude of habitat loss compared to the current extent of nearshore submerged habitat in the Boston Harbor region (MassGIS website).

Seafloor sediment map
Figure 3: Seafloor sediments of Boston Harbor where brown is hard bottom, red is gravel, orange is gravelly sediment, yellow is sand, and gray is mud (USGS/NOAA/CZM/DMF)

Currently, nearshore submerged habitats in the Boston Harbor area are a mosaic of the five substrate types and the species which thrive on and in them. According to sediment data derived from NOAA, CZM, USGS and DMF, the composition of Boston Harbor is dominated by mud (35%), sand (29%), and hard bottom (25%). Hard bottom includes cobble, boulder, and ledge features. Gravel (7%) and gravelly sediment (4%) comprise the rest of the area’s substrate. The high percentage of mud bottom is likely due to the number and size of rivers emptying into Boston Harbor carrying sediment laden runoff. Also the shape of Boston Harbor lends itself to low energy areas that are protected from strong ocean currents, where sediments more readily settle out and collect on the seafloor. The majority of hard bottom is located beyond the river mouths in the areas of Boston Harbor which are more readily flushed with stronger winds and currents.


As an urban environment, the Boston Harbor region hosts many active uses of the coastline and nearshore waters that threaten and adversely impact the nearshore submerged habitats. Threats to the nearshore habitats include physical impacts, changes in water quality, and the introduction of invasive species. The nearshore shallow habitat is physically impacted by activities that accompany busy, urbanized port areas – marine development (piers, revetments, and marinas) and moorings. The nearshore deep habitat is more commonly threatened by dredging and mining activities. These physical impacts usually result in a loss of habitat.

Both the nearshore shallow and nearshore deep habitats are also adversely impacted by activities which affect the water column above the seafloor. Historically, water quality in Boston Harbor was poor due to the discharge of raw or insufficiently treated sewage and sludge. However, water quality in Boston Harbor dramatically improved with the construction of the Massachusetts Water Resources Authority’s (MWRA) Deer Island wastewater treatment plant. Discharge of sludge stopped in 1995 and treated sewage in 2000. MWRA has reported through their harbor monitoring program a reduction in algae growth, an increase in benthic species diversity, and an increase in oxygen levels (MassBays Program State of the Bays). Unfortunately, other threats to water quality remain. The City of Boston still has a large number of Combined Sewer Overflows (CSOs) that need to be remediated. The use of water for industrial activities such as wastewater treatment and heating and cooling can change the temperature of the water, effectively altering the local habitat and impacting organisms. Industrial water use can also result in the loss of aquatic organisms through entrainment and impingement even with adequate precautionary measures. There are several industrial facilities in the study area that use seawater for industrial cooling and discharge heated effluent to Boston Harbor. These facilities are: General Electric in Lynn, Wheelabrator waste-to-energy facility in Saugus, Mystic Power Station in Everett, New England Aquarium and Gillette in Boston, and Twin Rivers Technologies in Quincy.

Invasive Tunicates
Figure 4: Invasive tunicates on boulder (P. Colarusso)

The last notable threat to nearshore submerged habitats in Boston Harbor is the introduction of aquatic invasive species. Aquatic invasive species displace native species by outcompeting them for suitable substrate, directly attaching to them, shading them from the sun, and/or threatening their food resources. Aquatic invasive species may be introduced to a system through a variety of vectors, many of which are present in the Boston Harbor region, including: commercial shipping, recreational boating, recreational fishing, aquaculture, and others (CZM Aquatic Invasive Species Program). Many varieties of aquatic invasive species have been found in Boston Harbor including European and colonial tunicates, star and sheath tunicates, green and Asian shore crabs, lacy crust and others through the CZM Aquatic Invasive Program (MIMIC survey results 2010).

Protection and Restoration Potential

Protection and restoration opportunities in the Boston Harbor Region for the nearshore shallow and nearshore deep submerged habitats primarily focus on protection through existing regulations and protection through information gathering efforts. Federal regulations offer protection of hard bottom communities. Additionally, some species, such as seagrass and shellfish beds, which inhabit the nearshore shallow habitat are also afforded regulatory protection. Also, areas used by finfish, such as winter flounder, during specific life cycle stages are offered regulatory protection through federal essential fish habitat designation. These protections are implemented as proposed marine development projects pass through regulatory reviews.

However, regulatory protections can only go as far as existing data allow. The nearshore deep habitat is varied and largely unmapped. The gathering of better and more detailed information is warranted for this habitat. Identifying and mapping data relating to rare species presence (i.e. soft coral), substrate composition, spatial distribution, finfish use, and marine invasive species presence would buoy protection activities. For example, a better understanding of the location of marine invasive species could lead to an understanding of the specific vectors which resulted in their presence. Mapping the foraging and refuge habitat for certain finfish species would allow for more targeted protection. The gathering of targeted information to inform protection initiatives is key to protecting the nearshore deep habitat.

Lobster on seafloor
Figure 5: Field of sand dollars (P. Colarusso)

Beyond mapping efforts, restoration opportunities exist for the nearshore shallow habitat. Restoration opportunities may be possible through the identification of physical impacts, improving water quality, and addressing marine invasive species stressors where applicable. Physical impacts to the nearshore shallow habitat can be caused by moorings, marinas, docks, piers, dredging activities, and coastal stabilization projects. By first identifying and mapping where these physical impacts overlap with high quality nearshore shallow habitat, they could then be targeted for restoration activities. Also, industrial uses and their adverse impacts to the substrate and water column should be identified. Upon locating these impacted areas, measures may be taken to improve or restore the habitat by addressing the specific stressors at that site. Improvements to stormwater treatment could also improve water quality. Lastly, the continued monitoring of marine invasive species in the nearshore shallow habitat could lead to restoration efforts to remove these species and restore native populations.

Literature Cited

Callaghan, Todd. 2011. Seafloor substrates. Personal Communication.

Massachusetts Ocean Management Plan. Volume 2. Baseline Assessment and Science Framework. December 31, 2009.

MassGIS website. Tidelands Jurisdiction (M.G.L. c.91) Datalayers from the MassDEP Waterways Program. March 2011.

Boston Harbor and Massachusetts Bay. Massachusetts Water Resources Authority (MWRA) Environmental Quality Department. Last visited November 30, 2011.

“Municipal Wastewater in Boston Harbor”. State of the Bays. Massachusetts Bays Program. December 2010.

Massachusetts Office of Coastal Zone Management Aquatic Invasive Species Program website.

Shepard, F.P., 1954, "Nomenclature based on sand-silt-clay ratios," Journal Sedimentary Petrology, v.24, p. 151-158.

Schlee, J., 1973. "Atlantic Continental Shelf and Slope of the United States sediment texture of the northeastern part," U.S. Geological Survey Professional Paper 529-L, 64 p.

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Boston Harbor Habitat Atlas
Updated 5/30/2012