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Recent water resources planning and management strategies state that the concepts of risk and variable inputs should be appraised in order to comply with multiple conditions. This becomes evident especially in environments with diverse uses of water, land use and climate change. In such a context, modelling of discharges and concentrations in rivers are valuable strategies to predict different scenarios. This research proposes an integrated analysis for modelling of flow and contaminant transport in rivers, based on hydrodynamics, time series, and water quality simulations. The first module estimates water volume and velocity, that have direct impact in pollutants transport; time series of concentrations are generated as synthetic pollutographs, using techniques based on flow conditions, time and statistical factors of a historical monitoring dataset - the objective is to match temporal scales of boundary conditions, since water quality data is usually available as irregular samples; the third module solves the advection-dispersion-reaction equation, exploring the different synthetic series as input. Results evidence that the input pollutograph, usually not explored in similar studies, may have a significant role in simulations for transport of substance in rivers under unsteady state; as consequence, corroborate with better estimates for planning strategies where temporal dynamic is relevant. The contributions lay the basis for further assessment of riverine systems linked to watershed dynamics, with multiple scenarios of data availability and input conditions.