The Indian River Lagoon (IRL) is a 156 mile long estuary that spans from Ponce de Leon Inlet in the north to Jupiter Inlet in the south. Located on Florida’s east-central coast, the IRL is America’s most diverse estuary. There are over 400 species of fish, 260 species of mollusks and 479 species of shrimp and crabs. The lagoon overlaps the temperate and the subtropical zones creating a highly diverse system.

The Mosquito Lagoon is long, narrow, shallow estuary that is bordered on the east by a barrier island and on the west by the mainland and is connected to the Indian River via the Haulover canal. The major community types are marshes or swamps, salt marshes, seagrass beds, drift algae, oyster bars, tidal flats, deep water areas, and spoil islands. There are several community types that border the aquatic preserve: coastal strand, secondary dunes, floodplain forest, hydric hammock and urban areas. During the 1950’s and 1960’s most marshes were rotary ditched for mosquito control purposes while others were impounded. Impounded salt marshes restrict tidal movement making them very susceptible to human impacts. Pollutants that enter this water body often remain there for extended periods of time without the aid of proper flushing.

Mosquito Lagoon has been designated an Outstanding Florida Water by the State of Florida and, as part of the Indian River Lagoon, an Estuary of National Significance by the Environmental Protection Agency.  It is renown for its outstanding biological diversity, recreational fishery and as habitat for several federally-protected animals.  Lagoon waters are classified as Class II which is suitable for shellfish (clam and oyster) propagation and harvesting.  All of these resources are dependent upon good water quality for their survival.  
While current data show that overall water quality in Mosquito Lagoon is good, several characteristics make the lagoon vulnerable to pollution.  Flushing is very limited - the only natural outlet is 10 miles north of the park.  The shallow average depth of only four feet allows bottom sediments to be easily stirred up by wind and storms.  The porous sandy soil does little to retain septic tank effluent and stormwater runoff from developed areas along the northwest boundary of the park.  In fact, when it rains more than 1.5 inches over a 24 hour period, fecal coliform levels rise to the extent that shellfish harvesting must be suspended for several days until the levels subside.  Recent installation of a sewer system in Bethune Beach and upgrading of the Edgewater wastewater treatment plant will be beneficial.  
 
Estuaries, such as Mosquito Lagoon, contain brackish water, a mixture of salt and fresh water.  In Mosquito salinity levels are high and frequently equal ocean levels (about 32 parts per thousand).  Because of this, several fish species spawn in the lagoon that normally spawn in the ocean.  Large influxes of fresh water from runoff or heavy rain can actually act as a pollutant, negatively affecting estuarine species sensitive to salinity levels. While a problem in portions of the Indian River Lagoon south of Canaveral National Seashore (CANA), salinity levels are relatively stable in Mosquito Lagoon, averaging from 28-34 ppt. 

  
Since the lagoon ecosystem is based heavily on healthy seagrass beds, water clarity is essential.  Grass beds require light to conduct photosynthesis.  Water that is clouded with silt or organic matter, including algal blooms caused by high levels of nutrients, prevent light penetration and limit the growth of seagrass.  Water clarity in Mosquito Lagoon is very good in the winter and early spring but decreases significantly in the summer and fall.