The water quality in the Limache stream was evaluated at five sampling stations during the period of low water flow. At each station, aquatic macroinvertebrates were collected and the following parameters were measured in situ: pH, conductivity, dissolved oxygen, and total dissolved solids. The biological oxygen demand, total phosphorus, and total nitrogen were determined in the laboratory. Water toxicity was determined through toxicity bioassays with the microalga Pseudokirchrneriella subcapitata. Thirty-three macroinvertebrate families were found and the dominant taxa were Dugessidae, Oligochaeta and Chironomidae. A significant correlation was found among the Family Biotic Index ChFBI, conductivity, and total dissolved solids (r = 0.92; p < 0.05). Species diversity was lowest, as was the growth rate of P. subcapitata, at the stations with the greatest anthropogenic activity and in the discharge zone of a domestic wastewater treatment plant.