Abstract Ostrovsky, I. 2009. The acoustic quantification of fish in the presence of methane bubbles in the stratified Lake Kinneret, Israel. – ICES Journal of Marine Science, 66: 1043–1047. Methane ebullition from bottom sediments is common in many productive bodies of water. During acoustic surveys, the methane bubbles can be mistaken as fish. In the stratified Lake Kinneret, the densities and target-strength (TS) values of acoustic targets were measured with a 120-kHz, dual-beam echosounder at night, when the fish schools were dispersed and single targets could be detected. The density and TS of methane bubbles were estimated in the anoxic hypolimnion, where there were no fish. A discrete-bubble model was applied in combination with a TS vs. methane bubble-size relationship to estimate the methane bubble TS at different depths. This information was used to quantify the densities of methane bubbles and fish, and the fish TS in the epilimnion where both types of target were found. During periods of rapid decrease in water level, methane bubbles could be the principal acoustic targets in the epilimnion, and their TS strongly overlapped that of fish. In some strata, they contributed up to 90–95% of all targets. The amount of methane bubbles in the water column depends on the type of sediment, bottom depth, and the history of sediment degassing. Their presence could be a serious obstacle to the accurate assessment of fish abundance in lakes and reservoirs with varying water levels, where intensive gas emission is a common feature. For such situations, backscattering by methane bubbles must be taken into account to avoid the erroneous quantification of fish abundance.