Submerged macrophytes are important components of wetland ecosystems in the Prairie Pothole Region of North America, but factors influencing species abundance and community structure are poorly known. We sampled submerged macrophyte communities and habitat characteristics in 18 prairie wetlands for five years in order to 1) assess interspecific relationships between macrophyte species, 2) test for presence of distinct species assemblages at the whole-basin level, and 3) identify relationships between community composition and limnological characteristics of the wetland basins. Macrophyte communities did not occur as distinct assemblages of species; most species showed eurytopic distributions, and communities varied along gradients of individual species abundances. Redundancy analysis showed that turbidity, presence/absence of fish, drainage history (restored versus non-drained), average depth, and surface area explained 20% of the variance in species abundance. However, turbidity and drainage history alone accounted for 15% of this variance. Most species showed a negative relationship with turbidity, while drainage history influenced community composition but had little effect on overall abundance at the community level. Our results indicate that restored and non-drained wetlands have similar species richness but differ in species composition. Species richness and total plant abundance in both restored and non-drained wetlands will be greatest in wetlands with low turbidity, moderate depth, and small surface area. However, substantial residual variation indicates that additional, unstudied factors are important determinants of community structure.