We analyzed interannual variability in a long-term record of chlorophyll concentration and phytoplankton species composition in the Rhode River, Maryland (USA). Over the approximately 30-year record, there was no long-term monotonic trend in phytoplankton chlorophyll concentration, though temporary directional trends related to precipitation patterns sometimes persisted for a decade before reversing. From counts on preserved samples, we estimated the dominance by different pigment-bearing groups and size classes. Diatoms, dinoflagellates, and cryptophytes comprised about 80–97% of the annual averaged class-specific biovolume. Cryptophytes dominated the first 2 years in the data set but displayed a long-term decline, after which diatoms dominated in all but four consecutive years in which there were large dinoflagellate blooms. There was a long-term increase in cells with equivalent spherical diameters from 4 to 10 µm, accompanied by declines in the proportion of cells in the 2- to 4- and 10- to 20-µm size classes. The main cause of these changes in size classes was a long-term increase in Chroomonas sp. and Apedinella radians and long-term decline in Microcystis sp. and an unidentified cryptophyte, respectively. These taxa were cosmopolitan in their seasonal and spatial distributions, and hence the long-term changes in taxa did not conform well with conceptual models based on succession of “life-forms.” The segregation of diatoms and dinoflagellates expected on the basis of “life-forms” applied to seasonal and spatial patterns. Characterizing the phytoplankton community in terms of diversity, size, and class-specific biovolume gave results that were consistent with one another and added insight to the broad-scale changes in chlorophyll concentration. Subtle changes in the size distribution of cryptophytes were not apparent from biovolume measures and would not have been apparent without microscopy. Though causes of such shifts may be difficult to identify, identifying the causes and predicting potential consequences cannot even be attempted without awareness of the phenomena.