Studies on crustacean communities in Chilean wetlands are scarce. The aim of this study was to characterize the crustacean community in forested wetlands from southern Chile and to establish their relation with the variations in the hydrological regime. In total, 540 samples were taken using three complementary sampling techniques in five wetlands during 2011 and 2012. The results show a total of four species of crustaceans, of which the amphipod Hyalella patagonica (Cunningham, 1871) (Hyalellidae) was dominant in ephemeral wetlands and the isopod Heterias exul (Mueller, 1892) (Janiridae) in permanent wetlands. The other species (the decapods Parastacus pugnax (Poeppig, 1835) (Parastacidae) and Aegla araucaniensis (Jara, 1980) (Aeglidae)) showed abundances below 6% in all wetlands. The identified crustaceans presented marked variations, both at a temporal scale and between wetlands with different hydrological regimes, both at the species level and at the crustacean community level. These patterns were mainly explained by changes registered in the annual hydroperiod and our results conform to the existing information that would indicate the importance of the inclusion of hydrological patterns in descriptions of freshwater communities.