Phytoplankton abundance and nutrient concentrations in shallow-water ecosystems are influenced by submerged macrophytes, zooplankton, and fish, but few studies have simultaneously assessed the influence of all three variables. We sampled 18 semipermanent prairie wetlands for 5 years to assess influences of minnows, submersed macrophytes, cladocerans, and drainage history on phytoplankton abundance and concentrations of nitrogen (N) and phosphorus (P). Our macrophyte data reflect the abundance of three distinct species assemblages (Chara, Potamogeton, and Myriophyllum assemblages) typical of these wetlands. Partial redundancy analysis showed only the Chara and Potamogeton assemblages and fish to be significantly related to algal abundance, N, and P. Macrophytes and fish together explained 40% of the total variance, but the Chara assemblage explained threefold, and the Potamogeton assemblage twofold, more variance than did presence/absence of fish. However, relationships with N and P differed for the two groups of macrophytes: P showed a strong negative relationship with both plant assemblages, and N showed a weak negative relationship with Chara but no relationship with Potamogetons. Our results indicate that phytoplankton and nutrient concentrations in prairie wetlands are strongly influenced by submersed macrophytes, although influences may depend on plant community composition.