The Patos Lagoon basin is a large (201 626 km2) and complex drainage system in southern Brazil. The lagoon is 250 km long and 60 km wide, covering an area of 10 360 km2. The exchange of water with the Atlantic Ocean occurs through a 0·8 km wide and 15 m deep inlet, fixed by 4 km long jetties, at the southernmost part of the Patos Lagoon. The estuarine area is restricted to its southern portion (10%), although the upper limit of saline waters migrates seasonally and year to year, influenced by the wind regime and river discharge. The known number of recorded limnetic fish species is 200, but this number is expected to increase. A higher endemism is observed in fish species occurring in upper tributaries. The basin suffers from the direct impact of almost 7 million inhabitants, concentrated in small to large cities, most with untreated domestic effluents. There are at least 16 non‐native species recorded in natural habitats of the Patos Lagoon basin, about half of these being from other South American river basins. Concerning the fishery, although sport and commercial fisheries are widespread throughout the Patos Lagoon basin, the lagoon itself and the estuarine area are the main fishing areas. Landing statistics are not available on a regular basis or for the whole basin. The fishery in the northern Patos Lagoon captures 31 different species, nine of which are responsible for most of the commercial catches, but only three species are actually sustaining the artisanal fishery: the viola Loricariichthys anus: 455 kg per 10 000 m2 gillnet per day, the mullet Mugil liza: 123 kg per 10 000 m2 gillnet per day and the marine catfish Genidens barbus: 50 kg per 10 000 m2 gillnet per day. A decline of the fish stocks can be attributed to inadequate fishery surveillance, which leads to overfishing and mortality of juveniles, or to decreasing water quality because of urban and industrial activities and power production. Global climatic changes also represent a major threat to the Patos system by changing the frequency of El Niño‐La Niña‐Southern Oscillation (ENSO).