Long term trends in the phytoplankton of the lower Chesapeake Bay were identified using flow corrected and uncorrected data sets, with 22 of 23 significant trends similar under both conditions. The major trends between 1985-1992 were for: 1) reduced phytoplankton concentrations; 2) decreasing numbers of phytoplankton taxa during spring, summer and fall months; and 3) seasonally mixed trends for diatom abundance in waters below the pycnocline, with spring months having decreasing densities, and increasing abundance trends in November and December. The flow patterns had different effects on the trends. Flow diminished the magnitude of the trends for total phytplankton concentrations, so these trends were greater in the flow corrected data. There were mixed patterns of influence when considering diatom abundance, with the presence of flow conditions showing greater trends for the number of taxa per sample.