Two techniques, the conventional purse seine method and a novel method using vertical hydroacoustic surveys at fixed positions, were applied simultaneously in the Gambia River estuary to sample a fish population. Environmental parameters were measured simultaneously. Four surveys were performed during different hydrological seasons to reflect the main sources of variation in the environmental conditions of the estuary. A total of 153 samples resulted from these surveys. To identify the environmental conditions in which the two methods yield similar pictures of the fish population, a regression tree was constructed in which the dependent variable was the difference between the standardised values of the catches from the purse seine and the estimated biomass from the acoustic samples. A highly significant correlation was found between the two approaches using a set of data (128 samples) that excluded the samples with specific environmental conditions (downstream samples with high transparency, and upstream ones with high transparency, high depth and high temperature). We conclude that, except under these specific environmental conditions, vertical hydroacoustic samples recorded at a fixed station can serve as a proxy of the catches from a purse seine and can allow the monitoring of fish biomass in estuaries without damaging the environment.