© 2014 Elsevier Ltd. Aquatic ecosystems are under increasing stress due to direct and indirect human activities. In response to this increased stress, aquatic ecosystems models are increasingly used to simulate water quality responses to changes. The increasing use of these models has not come without challenges. This thematic issue brings together examples of the latest thinking and novel approaches addressing key areas across a range of aquatic ecosystems, from lakes to rivers to marine waters. Topics include approaches applied to cover the full range of activities from methodological and technical developments of model-driven research of aquatic ecosystem functioning to model applications in lake management and decision-making. This thematic issue will provide additional momentum towards the ongoing development and improvement of aquatic models and their application.