Increasing demand for freshwater during the last century has so severely degraded many wetland ecosystems that they are some of the most seriously impacted environments in the world. Environmental flows are used as a management tool to restore parts of the hydrological regime altered by human water use, to rehabilitate these wetlands. Research and monitoring to date has focused on understanding ‘flow-ecology’ relationships, without investigating the mechanisms underlying them. We sought to understand how different basal food sources are incorporated into fish tissue in temporary wetland systems. This study provides a necessary first step toward the development of mechanistic research that investigates the effects of variation in fatty acids (FA) within the food and prey base on top predators. We added different sources of fatty acids to wetland mesocosms by adding extra food sources including redgum leachate to increase planktonic bacteria populations, cyanobacteria, green algae and biofilm matrix to observe how they were incorporated into secondary consumers. Wetland soil and water was added to replicate mesocosms, left for 28 days to produce zooplankton and then Western carp gudgeons added. There was a clear shift in the invertebrate assemblage structure following the introduction of the gudgeons. There was also a clear difference in assemblage structure and nutritional value between benthic and planktonic invertebrates. However, the addition of extra food sources did not generate differing FA profiles between treatments in the substratum fractions, invertebrates or fish after 14 days. We suggest that food sources generated within the mesocosms themselves may have outweighed any treatment effects. Using flooded wetland mesocosms potentially would have provided more realistic knowledge of the food web mechanisms of wetland inundation rather than feeding zooplankton fed specific primary food sources to fish. However, future experiments attempting to identify the mechanisms of the transfer of basal food sources in wetlands to secondary consumers may wish to directly feed fish primary consumers raised on specific basal food sources.