Display omitted •The Joint Danube Survey highlights the need for long-term, harmonised water quality data sets to facilitate management at a basin scale.•Long-term datasets can be used to optimise future monitoring programme design.•Large river basin monitoring programmes must respond to new challenges from emerging contaminants and future climate impacts. Effective management of water quality in large rivers requires information on the influence of activities within the catchment (urban and rural) throughout the whole river basin. However, traditional water quality monitoring programmes undertaken by individual agencies normally relate to specific objectives, such as meeting quality criteria for wastewater discharges, and fail to provide information on basin-scale impacts, especially in transboundary river basins. Ideally, monitoring in large international river basins should be harmonised to provide a basin-scale assessment of sources and impacts of human activities, and the effectiveness of management actions. This paper examines current water quality issues in the Danube River Basin and evaluates the approach to water quality monitoring in the context of providing information for a basin-wide management plan. Lessons learned from the monitoring programme in the Danube are used to suggest alternative approaches that could result in more efficient generation of water quality data and provide new insights into causes and impacts of variations in water quality in other large international river basins.