The focus of this study is on understanding salinity changes in the vicinity of the freshwater-saltwater interface in estuarine ecosystems. In these areas, species, habitats and ecosystems that are adapted to brackish conditions are expected to migrate in response to salinity changes under sea level rise. For the Avon Heathcote Estuary in Christchurch, an existing fine scale hydrodynamic model was available but not calibrated for salinity. A collaborative project was designed between the University of Canterbury and NIWA to calibrate the model and develop a scenario modelling approach for sea level rise at a level of resolution sufficient for understanding potential effects on important habitats. The purpose of this report is to provide a description of the model development process and an illustration of model outputs from an initial set of modelled scenarios for sea level rise.