With the aim to determine the water quality and trophic structure of aquatic insect communities in the rivers Zaratí and La Chorrera, a total of three sampling stations were established. Stations were set in a 40 Km transect ensuring the highest amount of habitats for aquatic insects. Stations consisted of different sections ranging from the high, median and lower parts of these rivers. At each sampling station, the sampling effort unit was consistent at one hour. Sampling campaigns were carried out during the month of April to August, 2014. A “D” net (500 ?m) was used to scan all habitats within the sampling stations. For the biological water quality analysis the following indexes were employed: Shannon-Weaver and EPT. The assignment of trophic functional groups (collectors-filters, collectors-gatherers, scrapers, predators and Shredders) was done primarily according to the specialized literature on neotropical taxa. For those neotropical taxa with no reference elsewhere, the proposed assignment by Cummins, et al., (2008) was applied. At the Chorrera river, 1434 individuals were collected; these were distributed in seven orders, 28 families and 47 genera. In the Zaratí river, nine orders, 33 families and 49 genera were found among the 1219 collected individuals. The most abundant orders were: Odonata, Hemiptera and Trichoptera. Predators dominated both in abundance and richness at the river assemblage level and transect level in both the Zaratí and La Chorrera rivers. The water quality showed moderate impact. According to our results the best biological index was the EPT (“Taxa”).