Estuaries are widely viewed as hotspots of primary productivity. The Coorong in South Australia is an inverse estuary divided into two lagoons, extremely important to the associated riverine, lacustrine and marine environments and characterized by a steep, lateral salinity gradient. Here, we analyzed the abundance and distribution of primary producers over two years (August 2011-2013) and investigated the biogeochemical factors driving observed changes. The phytoplankton community was numerically dominated by chlorophytes in the North Lagoon with Chlorohormidium sp. and Oocystis sp. being the most abundant species. In the South Lagoon, diatoms dominated the community, with Cylindrotheca closterium, Cyclotella sp. and Cocconeis sp. being the most prevalent species. Finally, cryptophytes and dinoflagellates were found to be present throughout both lagoons but in comparatively much lower abundances. Salinity was the most important driver of phytoplankton communities and ranged from 0.15 to 72.13. PSU between August 2011 and August 2013. Chlorophytes were found to be most prolific in freshwater areas and abundances rapidly declined laterally along the Coorong. Beyond a salinity threshold of 28. PSU, extremely limited numbers of Crucigenia sp. and Oocystis sp. were observed, but abundance were seven to ten-fold lower than in less saline waters. The salinity of the North Lagoon was found to be directly controlled by the flow volume of the River Murray, however, no effect of river flow on the South Lagoon was evident. Our findings suggest that management plans for the Coorong need to be put into place which can regulate salinity regimes via river flow, even during periods of drought. This is highly important in order to maintain low enough salinities throughout the North Lagoon, ensuring a continued healthy ecosystem state.