Phenotypic differences among species, even closely related species, may translate into distinct effects on ecosystem dynamics. In lakes, the generalist grazer genus Daphnia often has marked effects on the abundance of primary producers, the rate of primary production, and rates of nutrient cycling. The effects are particularly distinct during the clear-water phase (CWP) when algal biomass is driven to extremely low values as Daphnia densities undergo an annual population increase. Here we show that the timing of the CWP in Onondaga Lake, New York, USA, has depended upon which Daphnia species were present in the water column. An analysis of the ephippia and diapausing eggs from the sediments reveals that long-term changes in the zooplankton species assemblage tracks a history of chemical (especially salt waste) pollution. Prior to 1930 the assemblage was dominated by native D. pulicaria and D. ambigua. From 1930 to 1980, these species were replaced by D. exilis and D. curvirostris, two salinity-tolerant exotic species native to shallow salt pools of the southwestern United States and coastal brackish ponds of Europe, respectively. As industry was progressively shut down by government action over the period from the 1970s to the 1980s, the exotic species disappeared, and the two native taxa returned (plus D. galeata mendotae, which is also native to the region). As we have shown previously, the exotic species were identified either by hatching and rearing diapausing eggs (D. exilis) or by analysis of eggs using mtDNA (D. curvirostris). We interpret their role in seasonal algal dynamics in Onondaga Lake retrospectively using data collected in prior studies of the lake. The native Daphnia currently cause a typical spring CWP in late May and early June, whereas the exotic species caused an unusual late-summer (August-October) CWP during the period of maximum cyanobacterial density.