To examine how phytoplankton biomass and species' successions are influenced by multiple variables in the Swan River estuary, the four primary phytoplankton groups were modelled with a three-dimensional hydrodynamic model (Estuarine and Lake Computer Model; ELCOM) coupled with an ecological model (Computational Aquatic Ecosystem Dynamics Model; CAEDYM) to simulate physical and ecological processes in the Swan River estuary, Western Australia. The model was run using inputs of bathymetry, meteorological, flow and water quality data. The water quality data was collected weekly at nine sites along a 20 km domain of the Swan River estuary, from Blackwall Reach to Success Hill Reserve from October 1994 to July 1998 for this study.