Stubble farming (conservation farming, minimum tillage, zero tillage) has increased in Australia over several decades with claims of improved productivity, landscape stability and environmental benefit including ecosystem services downstream, yet recent audits show a dramatic and general decline in river health. This review explores explanations for this apparent anomaly. Many confounding factors complicate interactions between land use and river condition and may disguise or over-ride the potential benefits of adoption of stubble systems or other improvements in agricultural land use practice. These factors include climate change and variability; land use changes including an increase in bushfires, growth of farm dams and afforestation; lag times between land use change and expression of benefits in river systems; use of inappropriate scale that disguises local benefit; variations in the extent of ecosystem resilience; impacts of river regulation; and impacts of introduced species. Additionally, the value of river condition and utility is complicated by different local or regional perceptions and by contrasting rural and urban outlooks. The use of indicators, risk frameworks and biophysical modelling may help elucidate the complex relationships between land use and downstream ecosystem impact. The strengthening of local, regional and catchment scale approaches is advocated. This includes the re-integration of land management and governance with water management and planning. It is encouraging that farmers are themselves developing systems to optimise tradeoffs between on-farm activities and ecosystem service benefits. This approach needs to be supported and extended.