The effect of target strength oscillations, generated by surface or bottom-induced sound multi-pathing, can cause serious errors in estimates of fish biomass in horizontal acoustic surveys of extremely shallow inland waters (depth 1.7–2 m). In this study, the oscillations were shown to occur in both windy and calm weather conditions, and depended on the target’s depth and range from a transducer. In calm weather the oscillations were more pronounced and targets that were located close to the water surface and further from the transducer were most affected. Errors in target strength reached up to an 8 dB difference from the theoretical value. Fish abundance and size structure estimates are likely to be affected even more than biomass estimates. To avoid boundary-induced errors in target strength, simulations of fish biomass surveys demonstrated that the data-processing range should be limited to 10 m from the transducer for surveys conducted in extremely shallow waters.