Stones are stable substrates in streams, usually sheltering high richness and abundance of invertebrates. To investigate the structure of the Chironomidae assemblages associated with stones in a first-order stream located in an Atlantic Forest reserve in two periods of the year, stones with diameters from 10 cm to 25 cm were collected along a stretch of 100 m in riffle areas, during three months in the dry season and three months in the rainy season. The structure of the community was analyzed for each period through calculation of observed richness, Shannon's diversity (H'), and Pielou's evenness. The ordination of the samples from the dry and rainy seasons was evaluated by detrended correspondence analysis (DCA) and the presence of indicator species in the seasons was tested by IndVal analysis. The similarity in the faunistic composition between the periods was checked by ANOSIM. The results showed that, in general, the water velocity and rainfall were the abiotic variables that most strongly explained the abundance of larvae in the two periods studied, but the increase in these two parameters did not produce any significant effect on the richness and abundance of the fauna, suggesting stability of the stones for the Chironomidae community. There was a significant change in the faunistic composition (ANOSIM) and some samples had a stronger relationship with one of the seasons analyzed (DCA). The IndVal analysis indicated the characteristic taxa of each period, suggesting different responses to rainfall regimes. Besides this, Orthocladiinae were more abundant during the rainy season, while Chironomini was more abundant in the dry season. This study demonstrated the importance of the stones present in the stream channel as habitats for Chironomidae fauna, mainly in periods of high rainfall and water flow.