Poor water quality in lakes, rivers, estuaries and groundwater can be attributed to indirect effects of agricultural land use. Land management practices that lead to excess nutrients, sediment, pathogens and agrochemicals reaching waterbodies, or that negatively affect the hydrology, habitat and structure of waterbodies, can degrade water quality. This chapter describes farm and landscape management practices that can potentially prevent or mitigate adverse water quality impacts. Some examples of improved catchment water quality in response to changes in agricultural management are reported. Challenges associated with collecting evidence of the effects of agricultural management on water quality at the catchment scale, the potential for pollution-swapping, the cost-effectiveness of mitigation practices and approaches to governance of water quality management are also discussed.