Aim This work aimed to analyze the effectiveness of protected areas (PA) as maintainers of the fauna of benthic macroinvertebrates and the use of these in the water management of these areas. We tested the hypothesis that in streams located within the PA there will be greater abundance and diversity of organisms. Methods We collected macroinvertebrates in streams located inside and outside two PA in Southern Brazil: (Fritz Plaumann State Park, Santa Catarina, Teixeira Soares Municipal Natural Park, Rio Grande do Sul). In each stream we measured physical and chemical variables of the water. Three sub-samples of macroinvertebrates were collected on stony substrate with a Surber sampler and calculated abundance of organisms, rarefied richness, Shannon diversity and Evenness. Results The streams located in the interior of the PA presented well oxygenated waters and slightly basic pH. The electrical conductivity was higher in the external sections than the UC. We observed that rarefied richness, Shannon diversity and equitability were higher in the streams located inside the PA. PerMANOVA indicates that the composition was different between streams sections (p = 0.03) and PA (p = 0.01). Conclusions The use of organisms as bioindicators showed a potential response to the environmental integrity of streams. Thus, these organisms have potential for use by PA managers for monitoring and decision making on the maintenance of protected areas.