The relatively low biodiversity and simple hydrodynamics make solar salt ponds ideal sites for ecological studies. We have studied the ecological gradient of the primary ponds at the Shark Bay Resources solar salt ponds, Western Australia, using a coupled hydrodynamic ecological numerical model, DYRESM–CAEDYM. Seven ponds representative of the primary system were simulated with salinity ranging from 45 to 155 ppt. Five groups of organisms were simulated: three phytoplankton, one microbial mat plankton, and one zooplankton as well as dissolved inorganic and particulate organic nitrogen, phosphorus, and carbon. By extracting the various carbon fluxes from the model, we determined the role that the introduced zooplankton, Artemia sp., plays in grazing the particulate organic carbon (POC) from the water column in the high salinity ponds. We also examined the nutrient fluxes and stoichiometric ratios of the various organic components for each pond to establish the extent to which observed patterns in nutrient dynamics are mediated by the presence of Artemia sp. Model results indicated that Artemia sp. grazing was responsible for reduced water column POC in the higher salinity ponds. This resulted in an increase in photosynthetic available radiation (PAR) reaching the pond floor and consequent increase in microbial mat biomass, thus demonstrating the dual benefits of Artemia sp. to salt production in improved quality and quantity. In contrast, this study found no direct link between Artemia sp. and observed changes in planktonic algal species composition or nutrient limitation across the salinity gradient of the ponds.