In northeast Corrientes Province, there are more than 50,000 semi-rounded shallow rain-fed lakes. Several lakes have been disturbed mainly because urbanization causes eutrophication due to the illegal discharge of wastewater. We compared 22 metrics based on the structural attributes of macro-invertebrates associated with Egeria najas across seasons between five lakes with different human disturbance levels. Sixty-six samples of E. najas and associated invertebrates were collected seasonally using a net with an area of 962 cm2. A total of 17,737 macro-invertebrates of eight major groups, 35 families and 30 genera were recorded. The total macro-invertebrate abundance (number of individuals per plant dry weigh) and the family richness were significantly higher in less disturbed lakes than those under human disturbance, but the differences between seasons were not significant. Non-metric multidimensional scaling analysis differentiated the macro-invertebrate abundances between the more and less disturbed lakes; instead, the diversity indices were not useful for measuring the changes in the studied lakes. Besides, total number of taxa, number of EOT (Ephemeroptera, Odonata, Trichoptera) taxa, abundance and proportion of Trichoptera and abundance of Chironomidae reflected significant differences between the more and less disturbed lakes. Our results suggest that seven invertebrate metrics respond to urbanization, and they could be used to assess biological integrity of the studied lakes in complement of chemical monitoring of water quality. Management efforts should focus on the maintenance of macrophyte stands that provide high invertebrate diversity, which serve as food for a wide variety of fish.