A recent decline in wild rice (Zizania palustris) wetlands has been observed. We assessed the factors significant in understanding the distribution of Z. palustris and the surrounding macrophyte community. Sixty historic wild rice wetlands that currently display a wide range of rice densities were sampled in Wisconsin and Minnesota (USA). Chemical and physical factors and aquatic plants densities were measured. Data were analyzed using Canonical Correspondence Analysis in which the following trends were found. Wetlands that exhibited the greatest loss of Zizania tended to have higher levels of residential development within their watershed, ammonia, pH and depth. The aquatic plant community also shifted to plants that likely benefited from increases in light and pollinators. Increased agriculture was correlated with higher nutrient levels and increases with floating plants that can acquire nutrients directly from the water column. This study suggests optimal conditions for wild rice as well as the aquatic plant communities that are associated with these conditions. This paper demonstrates that Zizania (and other aquatic plants) may be very sensitive to small changes within their watershed that are typical of moderate development. Future management strategies should include consideration of these land-use patterns.