The eutrophication of surface waters has become an endemic global problem. Nutrient loadings from agriculture are a major driver, but it remains very unclear what level of on-farm controls are necessary or can be justified to achieve water quality improvements. In this review article, we use the UK as an example of societies’ multiple stressors on water quality to explore the uncertainties and challenges in achieving a sustainable balance between useable water resources, diverse aquatic ecosystems and a viable agriculture. Our analysis shows that nutrient loss from agriculture is a challenging issue if farm productivity and profitability is to be maintained and increased. Legacy stores of nitrogen (N) and phosphorus (P) in catchments may be sufficient to sustain algal blooms and murky waters for decades to come and more innovation is needed to drawdown and recover these nutrients. Agriculture’s impact on eutrophication risk may also be overestimated in many catchments, and more accurate accounting of sources, their bioavailabilities and lag times is needed to direct proportioned mitigation efforts more effectively. Best practice farms may still be leaky and incompatible with good water quality in high-risk areas requiring some prioritization of society goals. All sectors of society must clearly use N and P more efficiently to develop long-term sustainable solutions to this complex issue and nutrient reduction strategies should take account of the whole catchment-to-coast continuum. However, the right balance of local interventions (including additional biophysical controls) will need to be highly site specific and better informed by research that unravels the linkages between sustainable farming practices, patterns of nutrient delivery, biological response and recovery trajectories in different types of waterbodies.