In this special issue, we are able to present a selection of high-level contributions showing the manifold aspects of the monitoring, modeling, and management of water quality. Monitoring aspects range from cyanobacteria in water using spectrophotometry via wide-area water quality monitoring and exploiting unmanned surface vehicles, to using sentinel-2 satellites for the near-real-time evaluation of catastrophic floods. Modeling ranges from small scale approaches by deriving a Bayesian network for assessing the retention efficacy of riparian buffer zones, to national scales with a modification of the MONERIS (Modeling Nutrient Emissions in River Systems) nutrient emission model for a lowland country. Management is specifically addressed by lessons learned from the long-term management of a large (re)constructed wetland and the support of river basin management planning in the Danube River Basin.