Macroinvertebrate communities in alpine streams have rarely been examined over more than two consecutive years or at sub-monthly temporal resolution during the summer melt season, in relation to a range of stream physicochemical habitat measurements. This paper addresses these research gaps by investigating the inter- (late melt season, 1996-2003) and intra-annual (bi-weekly; June-September, 2002-2003) community compositional stability and persistence of three alpine streams fed from different water sources (snow, glaciers and groundwater) in the Taillon-Gabiétous catchment, French Pyrénées. Inter-annual community stability and persistence decreased from 1996 to 2003; however, groundwater stream communities changed less than those in the main glacial stream. Intra-annual community stability varied spatially and temporally, particularly in relation to water quality variables (water temperature and suspended sediment concentration); water quantity (stream discharge) was less important perhaps due to taxa possessing adaptations to flow variability. The 15 most abundant taxa were consistently more stable and persistent than the entire stream community suggesting a common pool of taxa in these streams. Overall, the results support the view that streams originating from different alpine water sources are characterised by distinct benthic macroinvertebrate assemblages, and demonstrate the value of sampling at nested temporal scales (inter-annual to bi-weekly) for understanding how these stream ecosystems function.