This paper presents aspects of a research investigation into nutrient fluxes into and out of an important Irish estuary, Wexford Harbour, located in the southeast of Ireland. Details of the methodology applied, the data collection and analysis and the models used are outlined. In particular, the paper addresses modelling of chlorophyll-a production in the brackish waterbody and its dependency on light attenuation.There are three distinct stages to the research carried out: (i) collection, collation and analysis of physical, chemical and biological water quality variables; (ii) development, validation and application of a chlorophyll-a production model; (iii) development of a Geographic Information System.The nutrient and chlorophyll-a production model simulates nine interactive water quality parameters; during the first stage these above parameters were measured to provide initial conditions for the model and for calibration purposes. From measurements, relationships were derived between the water quality variables and salinity, which were used to specify initial spatially varied values of the parameters to the model at different seasons. A relationship was also developed between light intensity, turbidity and concentrations of chlorophyll-a, based on field measurements. This relationship was incorporated into the model. The paper presents chlorophyll-a predictions using this relationship and illustrates how the enhanced model can be used as an accurate modelling tool for managing coastal ecosystems. The water quality model was incorporated into the ArcView GIs system providing an easy-to-use graphical user interface to run simulations and interrogate-results. (C) 2003 Elsevier Ltd. All rights reserved.