Freshwater coastal wetlands are vulnerable to impacts from increasing salinity due to sea level rise and other sources. This experiment examined the impact of increasing salinity on the quality of the food resources in tropical freshwater food webs using mesocosms. Fifteen 450L mesocosms were allocated to one of three treatment salinities: freshwater (0ppt), low salinity (3ppt), and high salinity (20ppt). The mesocosms were set up with sediment, algae, plants, invertebrates, and small freshwater fish from tropical freshwater wetlands in northern Australia. The mesocosms were kept at their target salinities for seven weeks with algae and invertebrates sampled on weeks two and four, and all groups sampled at the end of the experimental period. The fatty acid profiles of phytoplankton, benthic algae, macrophytes, zooplankton, macroinvertebrates and fish were analysed. Results showed differences in primary producer and consumer fatty acid profiles under different salinity concentrations and shifts in species richness. Since higher level consumers must gain essential fatty acids through the food web via algae and other sources, our results suggest that sea level rise may induce bottom-up trophic cascades and reduce species richness in freshwater wetland food webs.