One of the most problematic fishing methods in terms of by-catch and discarding is prawn-trawling. This paper analyses the incidental catch of an artisanal trawl fleet during two discrete Artemesia longinaris fishery seasons (2002 and 2004). The fishery season of A. longinaris operates monthly and it takes place in the surrounding area of the Barra do Rio Grande. Sampling was carried out during the fishing season (April–December) always on the same artisanal trawl boat. An observer was included on-board to avoid loss of information due to discards made by the fishermen at sea. Fifty species were caught: 38 fish and 12 crustaceans. Discrete fauna abundance and composition were recorded in analysed years, with higher by-catch ratios associated with elevated rainfall and low salinity. The overall discard ratio was 1:5.6, with values ranging from 1:11.3 in 2002 to 1:2.5 in 2004. The most striking differences between both years analysed were observed during autumn (1:75 in 2002 and 1:11.30 in 2004) and winter (1:16 in 2002 and 1:0.97 in 2004), while spring presented similar values (1:8 in 2002 and 1:4 in 2004). The discard ratio estimated in terms of number showed a different pattern, presenting overall values of 1:2.24 in 2002 and 1:0.5 in 2004. Higher estuarine runoff may have increased biomass production in the surrounding area of Patos Lagoon during 2002, sustaining higher abundance of estuarine-related and marine species in the area, as well as higher mean trophic level and abundance of top-predators. Conversely, A. longinaris production was consistently lower, since this marine species does not tolerate marked reductions in salinity. In 2004, salinity was higher, associated with low rainfall and favouring A. longinaris abundance in the area. During this dry year, the target-species was dominant in samples resulting in very low by-catch ratios, especially in winter (1:0.97). The catch was mainly composed of juvenile fish, since fishery is performed in nursery grounds.