Agriculture is associated with many of the leading threats to freshwater ecosystems, which are the most threatened environments on Earth. The overarching goal of my dissertation was to advance our understanding of the relationships between agricultural landscape structure and aquatic biodiversity and water quality, to identify potential management options for farmland aquatic ecosystems. In Chapter 2, I investigated the responses of anurans to agricultural landscape structure, with the particular goal of testing predictions about the influence of farmland compositional and configurational heterogeneity. I found that, while forest cover was the strongest predictor of anuran richness and abundance, farmland configurational heterogeneity was also positively related to abundance. In Chapter 3, I investigated the direct and indirect relationships between agricultural landscape structure and different physicochemical and biological measures of water quality in farmland drainage ditches. I found that physicochemical water quality was most strongly related to landscape composition, specifically, amounts of forest cover and high-intensity crop cover in the surrounding landscape. I also found support for a positive direct relationship between a biological measure of water quality, macroinvertebrate richness, and configurational heterogeneity, and indirect relationships between macroinvertebrate richness and landscape composition. In Chapter 4, I examined whether macroinvertebrate traits can be used as reliable indicators of elevated levels of specific agrichemical pollutants in farmland drainage ditches. My results suggested that macroinvertebrate indicators are probably less efficient than rigorous chemical sampling for the monitoring of specific contaminants in farm wetlands. Taken together, my results suggest that landscape management to support farmland aquatic ecosystems should focus mainly on landscape composition; in particular, agri-environmental policies should aim to increase or maintain amounts of non-crop cover such as forest, and reduce or maintain low amounts of high-intensity crop cover. My results also suggest that increasing farmland configurational heterogeneity, through reducing crop field sizes/increasing edge density, can be an effective management option to enhance aquatic biodiversity in agricultural landscapes. In addition, my results indicate a need for more management actions in our region to reduce nutrient pollution, and stronger policies for routine water quality data collection, as well as establishment and enforcement of water quality standards.