Shrimp and demersal fish trawling gears were compared as methods for sampling the deep-water estuarine fish communities in the Clarence River, a large east Australian coastal river. Three sites at three separate locations within the river were sampled quarterly over a 2-year period with both nets. Of the 68 fish species captured during the sampling program, 47 were caught with both nets, 10 only in the shrimp trawl and 11 only in the fish trawl. Summed over the entire study, more fish and slightly more fish species were captured with the shrimp trawling gear, but estimates of mean CPUEs (combined over species) and fish species diversities were very similar using either net during most seasons and at most sites. However, the nets were highly selective for particular species, with Selenotoca mutifasciata, Mugil cephalus, Liza argentea, Herklotsichthys castlenaui and Acanthopagrus australis caught predominantly with the fish trawling gear and Philypnidon grandiceps, Ambassis jacksoniensis, Ambassis marianus and Arius graeffei caught mainly with the shrimp trawling gear. For some species, shrimp trawling gear caught larger numbers of smaller individuals. Although gear type affected species composition, data obtained from either net were useful in discussing the spatial variation in the estuarine fish communities. Overall, trawling, particularly with the shrimp trawling nets, offered an excellent monitoring tool for the deep-water estuarine fishes, although a combination of methods might be required for a comprehensive description of fish communities.