Soil fertility management through the application of synthetic fertilizer or livestock manures is crucial to maintaining the productivity and profitability of cropping systems. Little, however, is known about the response of weed communities to different livestock manure nutrient sources. As weed communities with increased diversity are considered part of more sustainable agroecosystems, it is necessary to find management practices that result in diverse weed communities of acceptable densities without negative impacts on crop productivity. Here, we monitored the effect of five nutrient sources, with similar goals for nitrogen (N) management, including synthetic fertilizer, liquid pig manure, two types of solid pig manure, and solid dairy manure on the weed community in a five-year (2008-2012) study. The abundance, species richness, Simpson’s diversity, Simpson’s evenness, and species turnover in weed communities were assessed over time. Crop biomass, mid-season plant-accessible soil nitrate-N, and pre-season soil phosphorus were determined. The application of liquid pig manure or synthetic fertilizer enhanced crop biomass likely through increased crop accessibility to N. The continued use of these sources of nutrients over time, contributed to low density, low species richness, and low diversity weed communities, particularly through the decline of broadleaf weed species. Liquid pig manure and synthetic fertilizer treatments were lower in weed density and diversity than solid manures. Solid manure treatments were associated with increased weed densities and reduced crop biomass; however, these nutrient source treatments resulted in more diverse weed communities. Regardless of the nutrient treatments, we observed drastic declines in weed community abundance, species richness, and diversity in drier years. Our study suggests that a management practice that increases the accessibility of N to the crop, possibly through a mixture of solid manures and synthetic fertilizers or liquid pig manure, may be ideal for promoting a profitable cropping system with decreased densities and improved diversity in weed communities. Technological advances that provide more precise placement of solid manures to increase the accessibility of N to the crop, may further contribute to achieving such profitable and multifunctional agroecosystems.