We analyse how salinity, acidity and erosion threaten the ecosystem services of food production and the regulation of water quality in the Murray–Darling Basin, Australia’s most important food producing region. We used the Drivers-Pressures-State-Impact-Response (DPSIR) framework, to show that each of these threats undermines the functioning of the Basin’s agro-ecosystems and the two major ecosystem services (four other ecosystem services are briefly considered). These threats are driven by natural processes (e.g. rainfall) and anthropogenic activity (e.g. land clearing), and this leads to pressures exerted by hydrology, nutrient cycles and wind. Satisfactory information is available on the state of acidity and wind erosion, but information on the state of water erosion and salinity is inadequate. The impact of these threats on food production was primarily by reducing crop yield, while the impacts on water quality were to increase sediment, salt and nutrient loads. Management responses were either adaptive or mitigative; the former targets impacts while the latter focuses on drivers and pressures. Most management responses involved trade-offs between ecosystem services, although some synergies were found. Scale and spatial variability strongly influence the selection of responses. Understanding the mechanisms underpinning land degrading threats and the associated relationships allows better assessment on impacts to ecosystem services.