Spatio-temporal variability of pollutants in the environment is a complex phenomenon that requires a combined approach for its analysis. Whereas data on measured levels of contaminants in various environmental compartments is essential, it is not always possible to monitor at the necessary frequency and with the adequate spatial sampling distribution to capture this variability. Therefore a modelling approach able to complement experimental data and close the gaps in the monitoring programs is useful for assessing the contaminant dynamics occurring at different time scales. In this work a 1D water column fate model has been developed and tested for Polycyclic Aromatic Hydrocarbons (PAHs). The model has been coupled with a simple ecological model that includes a bioaccumulation module. Afterwards, the model has been used to study the temporal variability of contaminant concentrations as well as the fluxes between compartments. The results evidence the complex coupling between spatio-temporal scales and its influence on environmental concentration levels.