Seasonal succession and interannual variation of modern diatom populations in Fallen Leaf Lake, Sierra Nevada, California, are characterized and discussed in relation to stratification, water quality, and inflow during spring runoff. Fallen Leaf Lake is a deep, transparent subalpine lake that undergoes a 5–6 month period of stratification and develops a deep chlorophyll maximum (DCM) dominated by diatoms. A seasonal succession was observed, where the early spring was dominated by Asterionella formosa, Fragilaria tenera-group (F. tenera and F. nanana), Tabellaria flocculosa strain IIIp, Aulacoseira subarctica, and Urosolenia eriensis. Asterionella formosa and T. flocculosa strain IIIp persisted into the summer, becoming dominant components of the DCM. In late summer, Cyclotella rossii succeeded the araphids in the DCM and persisted until deep mixing in the late fall. In winter, the lake is ice free and well mixed, and Au. subarctica was abundant in surface waters, along with Nitzschia and the other components of the spring bloom. Strong species partitioning occurred between the epilimnion and hypolimnion, and Handmannia bodanica was the dominant summer epilimnetic diatom in all years. During a 3-year period, we observed interannual variation in the species of dominant phytoplankton. These years also varied in the depth and development of stratification, development of snowpack in the watershed, and timing of spring melt. The maximum depth of the epilimnion ranged from 12.5 to 17.5 m, and the DCM varied from 30 to 40 m deep. The weakest epilimnetic development was associated with 2011, a year with unusually deep snowpack, wintery spring conditions, and late melting. During 2011, Fragilaria tenera-group dominated the phytoplankton, and water clarity was low. A considerable portion of dead lotic diatoms were suspended in the water column, washed in from higher in the watershed during spring runoff. The lotic fraction is a significant portion of surface sediments and may be a useful proxy for identifying past changes in inflow. In addition, ratios of H. bodanica and C. rossii are explored as a possible proxy for strength in stratification. Collectively, these data provide a solid picture of the seasonal and interannual dynamics of the modern lake system, an essential step in evaluating the climate potential of the diatom record, which is currently being analyzed from lake cores.