An efficient method to investigate which morphological changes have greatest impact on the water quality is to carry out a computer modelling exercise. In this study, three models, a hydrodynamic (DYNHYD), a eutrophication model (EUTRO), and a sediment and micro-pollutant transport model (TOXI), were coupled together in the High Level Architecture (HLA) platform. DYNHYD dynamically simulates the propagation of a wave through a river reach one-dimensionally by solving the full dynamic wave equation. Important parameters that describe the river morphology are the roughness coefficient and the weir discharge coefficient. EUTRO simulates the phytoplankton-nutrient dynamics in water bodies with variables and parameters that regulate the process in this cycle. Examples of some of the more important parameters are the oxygen reaeration, phytoplankton growth or nitrification rates. TOXI was implemented to simulate the transport of sediments and heavy metals in which the most important transformation process of the metals was sorption. It is the aim of this study to see the effect that hydrodynamic parameters such as weir discharge and roughness coefficients have on water quality constituents, such as chlorophyll-a, dissolved oxygen and levels of ammonium and dissolved zinc.