Threats to Aquatic Habitat

The condition of aquatic resources, and the habitat they provide for species in the Neponset River Watershed, is affected by a variety of factors and activities in the landscape.

Pollutants; low water levels; direct removal of habitat; disturbance of vegetation and soil at the water’s edge; exotic, invasive species; acid precipitation; obstructions (dams); and degradation of fish spawning habitat all impact the watershed.

We’re here to help!

  • Is there a waterbody in your neighborhood with low water levels or pollution issues?  Please contact Environmental Scientist, Chris Hirsch, at 781-575-0354 x302 or
  • Is there a small, deteriorating dam on your property or down the street that could be removed? Contact Executive Director, Ian Cooke at 781-575-0354 x305 or


Pollutants can enter the water from the surrounding landscape, from precipitation, from groundwater, or from upstream in the water, and can directly kill wildlife or cause them hardship. High nutrient levels from untreated sewage can spark dense aquatic plant growth in waterways.

Water pollutants may include lawn care chemicals, sewage, motor vehicle oil, ice-melt chemicals, and historical pollutants that can leach into waterways from old spills, or release into the water from old sediments, like PCBs – the manufacture of which was banned since 1979, and DDT -use banned since 1972.

Low water levels

As water withdrawals continue to increase – pulling from groundwater and surface water resources, instream water levels drop, yielding “low flow” conditions that  concentrate aquatic pollutants, increase water temperatures, decrease dissolved oxygen levels, leave fish, fish eggs, and aquatic plants high and dry, and block fish passage.

In addition, the increased periods of drought associated with climate change yield low in-stream water levels.


Direct removal of habitat

Removal of riparian habitats and buffers reduces the ability of a waterway to maintain cooled water, to provide food and wildlife habitat, and to avoid pollution from surface water and erosion.

Channelization and hardening of river channels (with cement, riprap, seawalls, etc.) also simplify river structure and reduce instream habitat. Boat moorings can remove submerged aquatic vegetation.

Water joining the waterbody can cause bank erosion and siltation, which can kill fish eggs and block fish passage.

Disturbance of vegetation and soil at the water’s edge

Bank disturbance can cause siltation in the waterbody, warming of the water via removal of bank vegetation that shaded the water, and water pollution.

Presence of exotic, invasive species

Exotic, invasive species can change the characteristics of the waterbody, the aquatic food web, wildlife dynamics, and food availability, making the waterbody less suitable as habitat. Learn more about exotic, invasive species.

Acid precipitation

Acidic rain and snow occurs as a result of pollutants that have been released into the air via burning coal and smelting metal sulfide ores to obtain zinc, nickel and copper, as well as via volcanic eruptions, organic decay, and ocean spray.

An acidic rainstorm or snowstorm can cause temporary high acidity in waterbodies and also cause aluminum to leach from the surrounding landscape, into the water.

Aluminum is toxic to aquatic wildlife. The more acidic a waterbody becomes, the fewer species can live in those waters. However, it is also true that different aquatic species can tolerate different pH (i.e., Frogs withstand more acidity than can clams. If water becomes too acidic, fish eggs won’t hatch, and some fish can die.).


Waterway obstructions, such as dams or large debris, can modify waterflow, thereby raising water temperature, decreasing dissolved oxygen, reducing fish and other wildlife passage, and causing sediments and contaminants to settle.

Some aquatic species cannot tolerate the warmer, more polluted water, with less available oxygen, nor can they tolerate not being able to migrate. Low water levels, inadequate culverts and fish ladders, and accumulation of sediments can also obstruct waterways.

Degradation of fish spawning habitat

Pollution degrades migratory fish spawning grounds, as do lack of water, lack of appropriate substrate and damaged habitat.

Other spawning habitat threats include: removal of riparian habitats, erosion, sedimentation, hardening of river channels, decreases in submerged aquatic vegetation, increases in algae, and acid precipitation. Environmental changes due to climate change compound these issues.

Click here to read about fishkills.