Here we present a total of 86 stations sampled in six different areas along the Western Australian Coast in the southeastern Indian Ocean. This dataset includes measurements of planktonic net community production (NCP), gross primary production (GPP) and community respiration (CR) off coastal, estuarine and open ocean surface (0.5–3 m) waters between 15º - 36º South and 107º - 122º East. We also reported the following data for each station: temperature (ºC), salinity, nitrate (µM), phosphate (µM), chlorophyll-a (mg/m³), heterotrophic prokaryote abundance (cells/ml), Synechococcus abundance (cells/ml), picoeukaryotes abundance (cells/ml) and Prochlorococcus abundance (cells/ml).