The description of intertwined ecological processes in surface waters requires a holistic approach that accounts for spatially distributed hydrological/water quality processes. This study describes a new approach to model dissolved oxygen (DO) based on linked hydrodynamic and closed nutrient cycle ecological models. Long term datasets from the River Dommel (Netherlands) are used to determine: 1) if this methodology is suitable for modelling DO concentrations, 2) the model sensitivity to various levels of nutrients input, and 3) the DO production and consumption processes and their response to nutrient input changes. Results show that seasonal dynamics of DO are well quantified at long timescales; the sensitivity of DO to different pollutant sources exhibits significant seasonal variation and the largest influences on DO are aeration and mineralization of organic material. The approach demonstrates an ability to consider the impacts of nutrient input and long term vegetation maintenance on ecological quality.