The primary objective of this research was to develop a generic methodology for numerical modelling of the water quality within estuarine systems; in particular, this research focused on modelling nutrient dynamics and phytoplankton growth. This paper presents details of the developed modelling methodology and its application to Cork Harbour, an Irish waterbody that regularly experiences algal blooms. Input data requirements and, in particular, an innovative method for the determination of spatially varying initial conditions are presented. Phytoplankton dynamics are highly dependent on light intensity; a novel formulation for the light intensity component of the phytoplankton growth module was therefore developed and implemented in the model. The formula, which relates light intensity to turbidity and chlorophyll-a concentrations based on field data, is shown to achieve good results. Phytoplankton predictions were validated in an unusual but very effective manner using remote sensing techniques. A flushing module was included in the model to provide insights into transport processes. The paper demonstrates how simple flushing models may be used as a more cost-effective alternative to full water quality models for identification of potential eutrophic waters. Results from the Cork Harbour model are used throughout to demonstrate the effectiveness of the modelling methodology.