Otter trawl surveys are frequently used to assess estuarine fish and macroinvertebrate communities. Although these surveys may have similar objectives and sampling areas and seasons may overlap, the sampling gear is usually unique to the agency conducting the survey. An example of this is the North Carolina Division of Marine Fisheries (NCDMF) and Environmental Monitoring and Assessment Program-Estuaries (EMAP) surveys in North Carolinian estuaries. We estimated experimentally the selectivity and efficiency of the trawls used for these surveys to determine the comparability of data used to estimate community structure and the abundance of dominant species. The catch percent similarity of the trawls was low (12.0%). The NCDMF net (3.2-m flat otter trawl, 6.4-mm mesh body, 3.2-mm cod-end, plus tickle chain) precisely (11.7%) and accurately (4.5%) sampled brown shrimp, Penaeus aztecus, density but overestimated spot, Leiostomus xanthurus, densities (22.8% accuracy), possibly because these fishes had highly contagious distributions. The EMAP net (4.9-m high-rise otter trawl, 38.1-mm mesh body and cod-end) was precise (17.9–37.4%) but inaccurate (76.8–97.2%), probably because of the single large mesh size and the lack of a tickler chain. Our study suggests the EMAP and NCDMF surveys collect different subsamples of the same fish and macroinvertebrate estuarine populations, and therefore could deliver different results and conclusions.