As areas where salt and fresh water meet, estuarine ecosystems are complex and highly dynamic natural environments. Because of this, assessing fish densities in such areas is challenging. Hydroacoustics is rarely used to analyze fish populations in large estuaries, even though such approaches have in the past proven effective in providing information on fish distribution, abundance and size-structure in other aquatic systems. In this study, we compare densities detected acoustically with those obtained using traditional fish sampling methods in the Gironde estuary (France), where regular monitoring surveys using fishing gear have been carried out since 1979 to track ecological changes. With the aim of complementing traditional fish sampling, our study used vertical beam mobile acoustic surveys at 70 and 120 kHz between May 2010 and June 2012. There was a highly significant correlation between fish densities obtained with traditional fish sampling and those obtained using hydroacoustics. Both inter-annual variations and the timing of peak densities were similar for the two methods. This shows that the less labor-intensive acoustic method can be used to monitor estuarine fish populations. However, there is a need to develop internationally-accepted standards for collection and analysis of these data in order to ensure comparability of results across systems.