If reservoirs act as barriers to macroinvertebrate gene flow, reservoir size and species dispersal ability are likely to influence the magnitude of genetic differentiation between habitat fragments. We studied the genetic structure of two caddisflies (Stenopsychidae: Stenopsyche marmorata, Hydropsychidae: Hydropsyche orientalis) and one mayfly (Ephemerellidae: Cincticostella nigra) using 52, 37, and 58 RAPD markers from 24, 24, and 8 populations, respectively. Pairwise θ indicated that H. orientalis and C. nigra populations were not differentiated at any of the 6 and 2 studied reservoirs, respectively. In contrast, S. marmorata populations were genetically fragmented across the 2 largest reservoirs (3.3 and 6.0 km²) but not the 4 smaller reservoirs (0.1 - 1.6 km²). The dispersal habits of S. marmorata, requiring upstream flight before oviposition, may result in more pronounced effects of fragmentation. Genetic diversity (H_exp) was positively correlated with larval density for the caddisflies S. marmorata (p<0.01) and H. orientalis (p<0.05), suggesting that the census size was an accurate proxy for the effective population size. Our results indicate that the magnitude of impact on the genetic structure of macroinvertebrate populations varies with reservoir size, dispersal mode, and larval density. We suggest that sampling several species in sympatry can provide a better understanding of general patterns.