Aim This work proposes the application and development of environmental quality indexes for the evaluation of tropical estuarine streams in different spatial scales. The main goal was to understand the biological responses of the ichthyofauna in relation to different spatial indices in each group of streams, according to their predominant land use. Our hypothesis is that the impact on the stream riparian zones and in the land use in adjacent areas to the stream interfere in the structure of the fish assembly. Methods The Physical Habitat Integrity Index (PHI) on the local scale (80.0 m) and the Microbasin Integrity Index (MII) on catchment scale (1.6 km radius) was applied in all streams. In parallel, fish collections with electric fishing equipment were carried out in the 80.0 m reach. With the data from the PHI, MII and ecological estimators (species richness and percentage of Poecilia reticulata), the Kruskal-Wallis non-parametric test and Dunn’s post hoc test were carried out to verify the differences between the groups of land use, followed by a linear and polynomial regression analysis with trend line to show a relationship among indexes used and the biological responses. Results We observed that all streams’ groups presented a high positive correlation among PHI and MII. However, ecological estimators did not respond to changes in land use linearly, but in the form of a parable in a polynomial regression. Conclusions Our main conclusion is that the use of indexes and estimators as tools for environmental assessment is an efficient way to assess the health of the streams. The results also show that the integration of local and spatial indexes reduces the distortions observed in the indexes in isolation.