The Santa Cruz River is the last freeflowing river in Argentinean Patagonia. Two dams are projected, and no comprehensive pre-impoundment study has been undertaken. The present study investigated macroinvertebrate communities along three different hydrological periods and at three river sections located upstream and downstream of future dams. Fifty-three macroinvertebrate taxa were identified, with the most abundant orders being Ephemeroptera, Plecoptera, Coleoptera, and Crustacea (particularly amphipods). Ordination methods (CCA) and generalized linear models (GLM) were applied.According to the CCA, the main environmental variables related to macroinvertebrate density were temperature, suspended solids, depth, and substrate size. For the GLM, the main factors associated with macroinvertebrate abundance were location and hydrological period, and variables with the highest influences were temperature, substrate size, current speed, and depth. We anticipate that dam construction will modify in-stream habitat conditions, leading to changes in (i) macroinvertebrate community structure and (ii) local fish abundance due to loss of key prey taxa.