During the early 1900s, more than 90% of the surface area of Cootes Paradise Marsh was covered with emergent vegetation; currently, less than 15% of the surface is covered with aquatic vegetation and the remainder is wind-swept, turbid, open water. The loss of emergent cover is significantly correlated with mean annual water levels that increased more than 1.5 m over the past 60 years. Species diversity and the percent cover of the submerged macrophtye community also declined dramatically after the 1940s, coincident with decreased water clarity and increased nutrients from pollution by sewage and stormwater effluent. Phosphorus levels in the marsh dropped ten-fold after the sewage plant was upgraded to a tertiary-treatment facility in 1978; however, there was no measurable improvement in water clarity, in spite of a decrease in chlorophyll concentrations. Long-term changes in the composition of the planktonic, benthic and fish communities accompanied changes in water clarity, nutrient status and macrophyte cover. Phytoplankton changed from a community dominated by diverse taxa of green algae and diatoms during the 1940s, to a less diverse community dominated by a few taxa of green and blue-green algae in the 1970s, then to a much more diverse community recently, including many taxa of green algae, diatoms and chrysophytes; however, because water turbidity continues to be high, and algae tolerant of low light levels are now very abundant. Daphnia, which were prominent during the 1940s (especially in the vegetated sites) were replaced in the 1970s by smaller zooplankton such as the cladoceran, Bosmina, and several rotifer species including Brachionus, Asplanchna and Keratella. In the recent survey conducted in 1993 and 1994, small-bodied forms still dominate the turbid open-water areas, while medium-sized cladocerans such as Moina were common near macrophyte beds. Generally, total herbivorous zooplankton biomass tended to be highest next to Typha beds and declined with increasing distance from the plants. Conversely, biomass of edible algae at these sites increased with distance from the macrophytes. Species diversity of aquatic insects declined dramatically over the past 40 years, from 57 genera (23 families and 6 orders) in 1948, to 9 genera (6 families and 3 orders) in 1978, to only 5 genera (3 families and 2 orders) in 1995. The diverse benthic community present 5 decades ago has now been replaced by a community consisting primarily of chironomid larvae, oligochaetes and other worms associated with low-oxygen environments. These successional changes illustrate the impact of natural (fluctuating water levels) and anthropogenic (deterioration in water quality) stressors on the character of the biotic communities, and reveal the complex interactions among the various trophic levels and the abiotic environment as degradation and remediation proceeded.