A quick diagnosis of the ecological quality of five sections of the Macacu-Guapiaçu hydrographic complex was performed using visual assessment protocol (VAP), conventional analysis, composition and structure of ciliates and the occurrence of benthic macro invertebrates.Water samples were collected from five sampling stations (A-E) in July of 2010.Protists were sampled with aid of artificial substrates, and macro invertebrates were sampled using the multi-habitat method.A total of 22 taxa of protozoa and 51 taxa of macro invertebrates was registered at the five stations.Reference station (A) showed greater protist diversity and higher values of BMWP-CETEC and IBE-IOC indices relating to macro invertebrates.The impacted stations (B and E) presented lower diversity and higher abundance of protozoa, as well as the lowest values for the rates.The four methods used were convergent to diagnose reference station (A), the impacted stations (B and E) and those in intermediate conditions (C and D).Thus, the methods were complementary, as the conventional parameters and ciliate assembly were more sensitive to detecting the increase in organic pollution and VAP and macro invertebrate assembly detected changes in geomorphology and habitat degradation.