The Lake Worth Lagoon is a major estuarine water body located in Palm Beach County, Florida whose remaining natural resouces need to be protected. The lagoonal ecosystem has been stressed through the past one hundred years due to many anthropogenic influences. Altered hydrology of the system allows massive freshwater discharges into the lagoon, which exit via two ocean inlets and influence continental reef systems. These discharges carry large influxes of nutrients, suspended and dissolved organic matter, contaminants, and toxins into the lagoon, affecting the flora and fauna. Additional pressures in this urbanized coastal area include boating and fishing pressures, as well as loss of natural habitat through physical alterations to the system. A conceptual ecological model of the cause-and-effect relationships of flora and fauna to human-induced and natural conditions within the system was developed. The model consists of ecosystem external drivers and ecological stressors, ecological attributes, and ecological effects, and presents research hypotheses, including the effects of altered volume, timing and distribution of fresh water relative to seagrasses, macroinvertebrates, salinity, fishes, nutrients, toxins, suspended solids, and dissolved organic loads that will assist in the development of a quantitative hydrodynamic model for this system.