This study found a strong relationship between fin and muscle tissue in three Australian fish species, showing that non-lethally collected fin tissue can be used as a proxy for muscle tissue in isotopic trophic studies. We hypothesised that a strong linear relationship exists between fin and muscle δ13C and δ15N isotope ratios, and conversion equations can be developed where differences exist. We analysed fin and muscle tissues of three common species (Cyprinus carpio, Macquaria ambigua and Nematalosa erebi) from the Barwon–Darling River, New South Wales, Australia. There were significant differences between fin and muscle δ13C values for all species, and fin tissue was a good predictor of muscle tissue δ13C (r 2 = 0.77 for all species). The relationship between d15N values was less consistent, with a significant difference found in one species, but fin tissue was still a good predictor (r 2 = 0.72 for all species). Developing species specific tissue conversion models results in the least amount of error, but regional models result in similar error and are more accurate than general global models. These results are consistent with prior studies of different species. This study provides tissue conversion models for three species common to Australian lowland rivers, facilitating the inclusion of fish in food web studies with non-lethal collection methods.