Accurately estimating the biomass of carp in Australia is integral in determining the risks and success of the proposed release of the Cyprinid herpesvirus-3 (CyHV-3) as a biological method control of carp. Three methods; electrofishing, dual-frequency identification sonar (DIDSON) and side scan sonar (SSS) were evaluated in a small shallow lake, 2 metres deep and a large deep lake, average depth 50 metres. The results show benefits and limitations with all techniques. The DIDSON was able operate in turbid environments with less fish missed than electrofishing. DIDSON can determine the biomass of the fish community but was not able to differentiate species with similar body shapes. Both electrofishing and DIDSON methods were limited to the top 5 and 10 metres of water respectively and were unable to determine any fish biomass below these depths. The SSS was the only method able to identify total numbers below 10 metres deep but the system is not able to determine biomass. Both sonar methods are passive techniques thus eliminating fish handling and stress. It is recommended a combined approach would give the most accurate result for total biomass and electrofishing be used where speciation is required.