There is a growing need for strategic assessment of environmental conditions in river basins around the world. In spite of the considerable water resources, Brazil has been suffering from water quality decrease in recent years. Pardo River runs through Minas Gerais and São Paulo, two of the most economically important states in Brazil, and is being currently promoted as a future drinking water source. This study aimed at integrating three different tools to conduct a hydromorphological assessment focused on the spatial complexity, connectivity, and dynamism of the Pardo River, Brazil. Twelve sampling stretches were evaluated in four sampling campaigns, in dry and rainy seasons. In each stretch, permanent preservation areas (PPAs), hydromorphological integrity by rapid assessment protocol (RAP), and physicochemical parameters were qualified. The kappa coefficient was used to assess statistical agreement among monitoring tools. The PPA analysis showed that in all stretches, the vegetation was modified. RAP results revealed environmental deterioration in stretches located near human activities and less variability of substrates available for aquatic fauna and sediment deposition as well. Low values for dissolved oxygen in the river mouth were noted in the rainy season. Electrical conductivity was higher in stretches near sugarcane crops. The poor agreement (k<0.35) between the RAP and physicochemical parameters indicates that the tools generate different and complementary information, while they are not replaceable. Potential changes of the hydromorphological characteristics and variations in physicochemical indicators must be related to extensive PPA modification.