Seasonal changes in freshwater phytoplankton communities have been extensively studied, but key drivers of phytoplankton in saline lakes are currently not well understood. Comparative lake studies of 19 prairie saline lakes in the northern Great Plains (USA) were conducted in spring and summer of 2004, with data gathered for a suite of limnological parameters. Nutrient enrichment assays for natural phytoplankton assemblages were also performed in spring and summer of 2006. Canonical correspondence analysis of 2004 data showed salinity (logCl), nitrogen, and phosphorus (N:P ratios) to be the main drivers of phytoplankton distribution in the spring, and phosphorus (C:P ratios), iron (logTFe), and nitrogen (logTN) as important factors in the summer. Despite major differences in nutrient limitation patterns (P-limitation in freshwater systems, N-limitation in saline systems), seasonal patterns of phytoplankton phyla changes in these saline lakes were similar to those of freshwater systems. Dominance shifted from diatoms in the spring to cyanobacteria in the summer. Nutrient enrichment assays (control, +Fe, +N, +P, +N+P) in 2006 indicated that nutrient limitation is generally more consistent within lakes than for individual taxa across systems, with widespread nitrogen and secondary phosphorus limitation. Understanding phytoplankton community structure provides insight into the overall ecology of saline lakes, and will assist in the future conservation and management of these valuable and climatically-sensitive systems.