Stream insects use in different ways the stream habitats which affect patterns of species occurrence on stream. The nestedness is one of these patterns being an ecological mechanism that generates beta diversity. In this study, we verify the effects of temporal environmental variations on nestedness patterns of Chironomidae assemblages on subtropical streams. We collected chironomid larvae during winter and summer during three years (2010, 2011 and 2012) in Brazilian Subtropical low-order streams (Erechim, state of Rio Grande do Sul, Brazil). We measured environmental variables in each stream. To assess if assemblages will show nested patterns intra-and interannual we used a NODF metric. We observed nestedness only in one year, this pattern was due to variation of limnological factors, which are directly associated with climatic conditions (precipitation and water temperature) and agricultural management (e.g. dissolved oxygen and nutrients). Climatological events affect Chironomidae community through the time. The variations on precipitation values could be one of the mainly factors that influence nestedness for this community. Finally, studies on nesting on time scales should consider inter-annual comparisons, as climatic variations are more evident.