Resumo. Abstract: Aim In this study we validated a tool to assess and monitor streams ecosystems to subsidize future research, governmental surveillance and citizen science activities. Our primary objective was to (i) provide improvements and adaptations of the Rapid Assessment Protocol (RAP) proposed by Cionek et al. (2011) and provide a new RAP, and then (ii) evaluate the association among the RAP scores and limnological parameters. Methods The RAP was adapted to streams draining through a sandstone geological formation, and the final validation process was conducted in 30 streams. We used linear models and correlation analysis to understand the association of the RAP scores with in-stream limnological and physical parameters (n=30) and nutrient concentrations in the water (n=9), respectively. Two parameters have been adjusted according to our professional’s judgment which have provided feedback since 2011. Results The RAP scores explained 29% of the variability of in-stream limnological and physical characteristics of the streams. Streams with higher RAP scores were those with higher dissolved oxygen and higher depths. Streams with lower RAP scores were those with higher widths, conductivity, and turbidity. Streams with higher orthophosphate and ammonium loads were those with the predominance of slow and shallow flow regimes, while streams with higher nitrate concentration were those with straight channels. Limnological and physical indicators showed the same tendency of ecosystems quality (degradation or preservation), and yet are complementary because they evaluate distinct features of the system. Conclusions The RAP adapted for the Arenito Caiuá streams provide a good interpretation on the physical habitat features of streams and can be used both as a single diagnostic and monitoring environmental tool or a complementary tool along with limnological and biotic parameters.