An autoregressive approach for the prediction of water quality trends in systems subject to varying meteorological conditions and short observation periods is discussed. Under these conditions, the dynamics of the system can be reliably forecast, provided their internal processes are understood and characterized independently of the external inputs. A methodology based on stationary and non-stationary autoregressive processes with external inputs (ARX) is proposed to assess and predict trends in hydrosystems which are at risk of contamination by organic and inorganic pollutants, such as pesticides or nutrients. The procedures are exemplified for the transport of atrazine and its main metabolite deethylatrazine in a small agricultural catchment in France. The approach is expected to be of particular value to assess current and future trends in water quality as part of the European Water Framework Directive and Groundwater Directives.