This paper describes the results of the investigation of a shallow urban lake before, and a second year after, restoration to determine the effects of aeration and bottom-sediment removal on the trophic state and environmental variables controlling the lake's phytoplankton, macrovertebrates and zooplankton compositions. The anthropogenic eutrophic process of the lake is characterized by increased nutrient concentrations from urban run-off inputs. This addition triggers a chain of events that start with a massive increase in the growth of primary producers, as these are generally growth-limited by nutrients in freshwater ecosystems. Although the lake was artificially mixed, nuisance cyanobacteria were dominant as primary producers the second year after restoration, during the summers of 2004 and 2005, until this population collapsed and were replaced by diatoms after periods of high winds, rainfall and a decreased temperature. The absence of macrophytes in the main basin because of the removal of bottom sediment had a major effect on macroinvertebrates and zooplankton. Daphnia sp. was the dominant zooplankton species before restoration, being replaced by Bosmina sp., possibly because of the lack of refuge by macrophytes. As an alternative, Bosmina sp. used the surface blooms of cyanobacteria in summer as refuge from grazing by planktivorous fish. The greatest disturbance on the macroinvertebrate community richness and evenness was the decline of scrapers and shredders, because of the lack of macrophytes after removal of the lake bottom sediment.