Critical to management of regulated estuaries is understanding the influence of freshwater inflow on trophic dynamics. Considerable monitoring of biotic assemblages and investigation of fish diets occurred in the Coorong from 2003–2016, which encompassed highly variable freshwater inflow. This presented an opportunity to investigate food-web structure under contrasting hydrology. Conceptual food-web models, focussing on fish, were constructed for two hydrological periods: 1) ‘low inflow’ (<1,200 GL/yr); and 2) ‘high inflow’ (>5,000 GL/yr), based on data from 2003–2010 and 2010–2013, respectively. Semi-quantitative models were developed using: 1) species composition, abundance and distribution information from monitoring programs; and 2) dietary and trophic information from gut-content and stable isotope studies. Results identified that the Coorong food web is temporally and spatially variable. During low inflows and high salinities, a contraction of suitable habitat (<~55 ppt) was reflected in food-web structure. Diversity and abundances of macroinvertebrates and fish were highest in the Murray Estuary (ME) where salinities were marine, but declined into the North Lagoon (NL) and South Lagoon. Accordingly, feeding guild number and food chain length also decreased along this gradient. In contrast, favourable habitat extended far into the NL during high inflows. Models indicated a greater contribution of pelagic components of the food web, especially freshwater-derived, towards production in the ME and NL during years of high inflows, whilst transfer of energy to higher trophic levels during low inflows was primarily through the benthic pathway. This study reinforces that regular inflow to the Coorong is beneficial to the food web as it expands favourable habitat that supports high abundances and diversities of biota, and enhances productivity through food resource input. These models have the potential to be further refined and aid management of the Coorong.