An integrated 1-D mathematical model that simulates hydrodynamics and water quality in rivers and streams is briefly presented and applied. The model consists of a hydrodynamic sub-model (RISH-1D) and a water quality sub-model (RISQ-1D). RISH-1D is based on the Saint–Venant equations, which are discretized using the implicit weighted four-point Priessmann scheme and solved by the iterative method of Newton – Raphson. RISQ-1D consists of mass balance equations for the water quality variables of interest that are discretized using the second order accurate implicit Crank-Nicolson method and solved via the Thomas algorithm. The model is applied in Pinios River, in Greece, to investigate the effect of transient flow conditions on the concentrations of pollutants.