Recent research indicates that Lake Erie ecosystem health is declining due to increases in total phytoplankton biomass throughout the lake and the recurrence of cyanobacterial blooms in the western basin and nearshore areas of the central and eastern basins. In this paper, we use extensive information on phytoplankton and zooplankton communities collected from 1995 to 2003 to test whether the health of the lower trophic levels in the lake has indeed changed recently. We found that the lake’s total phytoplankton, inedible phytoplankton, cyanophyte, and total crustacean biomasses increased from 1995 to 2003 based on our samples, although linear regression analysis versus year did not fully support this conclusion. A crustacean taxonomic index also indicated the lake is eutrophic, particularly in the western basin. Overall, we found that plankton communities indicate that Lake Erie has better health than at the height of cultural eutrophication, but that the system remains impaired and it is less healthy than it was 10 years ago.