Phytoplankton abundance, composition, and productivity were monitored on a bi-weekly basis from March/ April through November/December at two offshore stations in southeastern Lake Michigan in 1983–1987, 1995– 1998 and 2007–2008 (exception 1983–1984 which were sampled from May to August). During the spring isothermal mixing period, surface-mixed layer (SML) chlorophyll a and phytoplankton biomass (carbon) and water column primary productivity decreased substantially in 2007–2008 as compared to 1995–1998 (66%, 87%, and 70% decrease, respectively). Smaller or no decreases were noted between 1983–1987 and 1995–1998 (chlorophyll a 23% decrease, phytoplankton biomass 5% increase, and production 22% decrease). Phytoplankton composition also changed during the spring isothermal mixing period in 2007–2008 as compared to 1983–1987 and 1995–1998; all phytoplankton groups with the exception of cyanobacteria and chlorophytes exhibited dramatic reductions in 2007–2008. The pronounced changes in phytoplankton properties during spring mixing in 2007–2008 were attributed to the filtering activities of the quagga mussel (Dreissena rostriformis bugensis). During mid- and late thermal stratification periods, SML phytoplankton chlorophyll a and phytoplankton carbon and water column primary production exhibited only one significant change across all decades (mid-stratification production in 2007–2008 as compared to 1995–1998 and 1983–1987). Phytoplankton compositional changes in the SML also were limited during thermal stratification. The size of the deep chlorophyll layer (DCL) in 2007–2008 was similar to or smaller than those in 1983–1987 and 1995–1998. However, phytoplankton composition in the DCL changed as net diatoms constituted < 5% of total phytoplankton in the 2007–2008 DCL but over 50% in 1983–1987 and 1995–1998.