Methane (CH4) in aquatic systems is usually associated with anoxic sediments or water columns of lakes and reservoirs. Very few reports have been made of CH4 biogeochemistry in flowing systems. Several CH4 seeps occur along the Condamine River in Queensland, leading to very high concentrations of dissolved CH4 in the water column. Methanotrophic microbes use CH4 as a source of carbon and energy, thus can potentially direct CH4 into aquatic foodwebs. To test this suggestion, we sampled sites where there was no recognisable CH4 generation and using a multi-analysis approach, made comparisons to seep sites with high concentrations of CH4. We used a multi-pronged approach, combining measures of instream primary and secondary production, stable isotope analysis and quantitative microbial community analysis to determine whether CH4 could fuel the riverine food web. Across all sites, a large part of the gross primary production was due to phytoplankton. Community respiration was variable across sites, with phytoplankton making major contributions at times, while at others, a large background CR was measured. Estimates of planktonic metabolism suggested heterotrophic organisms were making a major contribution to CR at the seep sites. Density measurements of zooplankton showed that the presence of CH4 contributed to the development of populations and influenced community structure. Quantitative estimates of methanotrophic bacteria showed community structure and numbers of organisms responded to the presence of methane. In final measures of carbon transfer, we showed that between 20-25% of the carbon of different biota was ultimately derived from the methane. This value peaked at up to 60% in small mayflies. Ongoing work is quantifying rates of methane-driven respiration and changes in benthic microbial community composition to the presence of new CH4.