We conducted hydroacoustic, gill‐net, and push trawl surveys to quantify changes in habitat‐specific fish size and biomass in shallow (<2‐m) estuarine waters of Barataria Bay, Louisiana, in order to evaluate essential fish habitat. Surveys were conducted monthly between June 2003 and May 2004 among regions located along a north—south salinity gradient. The fish length distributions derived from the gill‐net and push trawl catches showed moderate concordance with the measured target strength distributions, indicating that our integrated approach more effectively characterized the fish community than using only a single gear type would have. Acoustic estimates showed that biomass was highest during fall (mean ± SE; 2.30 ± 0.27 g/m3) and next highest in spring (1.49 ± 0.20 g/m3), with relatively low biomass during summer (0.70 ± 0.14 g/m3) and winter (0.86 ± 0.14 g/m3); pelagic fish biomass from nets was low during winter (53.9 ± 14.9 grams per unit effort [gpue]) but relatively high in fall (846.1 ± 207.2 gpue), spring (774.3 ± 175.5 gpue), and summer (620.3 ± 140.7 gpue). Oyster habitat supported a greater biomass of pelagic fish (acoustic survey: 1.54 ± 0.15 g/m3; gill‐net survey: 467.3 ± 81.0 gpue) than soft‐bottom habitat (acoustic: 0.94 ± 0.11 g/m3; gill‐net: 315.2 ± 54.8 gpue). Among regions, the greatest biomass of pelagic fish was observed at polyhaline stations (acoustic: 1.78 ± 0.19 g/m3; gill‐net: 654.3 ± 136.5 gpue), followed by mesohaline (acoustic: 1.18 ± 0.15 g/m3; gill‐net: 378.5 ± 79.1 gpue) and oligohaline stations (acoustic: 0.82 ± 0.12 g/m3; gill‐net: 228.3 ± 50.2 gpue). Gill‐net biomass was linearly related to the acoustic biomass estimates of small pelagic fish. The complementary, multigear approach proved to be useful in evaluating habitat use and may be particularly helpful in identifying and monitoring ecosystem reference points to evaluate change and in standardizing ecosystem‐based assessment approaches.