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Objectives of this paper were to examine and document pre-management water quality conditions on three oxbow lakes and resulting changes following the implementation of Best Management Practices within the Mississippi Delta Management Systems Evaluation Area (MSEA). Aquatic habitats have declined worldwide over the last decade. This decline can be attributed to the draining and clearing of these habitat areas for other agricultural uses. Non-point source pollution associated with agricultural runoff has also contributed to the decline in aquatic habitats. The Mississippi Delta MSEA is a competitive agricultural systems-based research project designed to address the problems associated with non-point source pollutants. This project is unique among MSEA projects because of its location in the Mississippi River alluvial plain and its strong ecological research component. Experimental design of the Mississippi Delta MSEA called for the development of structural and cultural treatments to reduce sediment and associated pollutants entering watershed oxbow lakes. Three watersheds within the project were selected and developed with different levels of best management practices (BMPs). Changes in lake water quality and fisheries characteristics were used as measures of management success. Analyses of water quality prior to the implementation of BMPs indicated lakes that were stressed and ecologically damaged due to excessive in-flowing sediments. Significant improvements in water quality were realized through the use of cultural and structural BMPs. Sediments were decreased 34 to 59%, while Secchi visibility and chlorophyll generally increased. The most dramatic improvements in water quality occurred in the two watersheds that featured cultural practices and combinations of cultural and structural practices, respectively. Reducing suspended sediment concentrations in these oxbow lakes resulted in conditions favorable for phytoplankton production. Increases in phytoplankton production resulted in increased chlorophyll concentrations and higher concentrations of dissolved oxygen, leading to improved secondary productivity. Results further indicated that cultural BMPS may play the more vital role in improving lake water quality and may be needed in addition to structural measures to ensure improved water quality in oxbow lakes receiving agricultural runoff.