This paper describes three datasets of seamless bathymetry and coastal topography for Sydney Harbour (Port Jackson), Botany and Bate Bays, and the Hawkesbury River. The datasets used to form these compilations were the most recent and highest quality available to the authors and were originally collated using the software ESRI ArcGIS. The original compilation of this data was undertaken to support tsunami modelling research by the authors of this paper. Before processing, all data were adjusted and/or reprojected to conform to the vertical datum Australian Height Datum (AHD) and horizontal projection WGS84 UTM zone 56. Data resolution and density was highly variable and grid resolutions of the final datasets were selected as the highest resolutions possible using the most sparse data in the compilation in question. For areas where no data were available, the ESRI ArcGIS interpolation tool, Topo to Raster, was used to provide a best estimate. These dastasets of three important Australian waterways provide a useful tool for coastal research and scientific interest.