Parasites can influence host population dynamics and genetic structure; thus, it is crucial to study parasite distribution among and within host populations. We explored spatial infection patterns in Daphnia longispina complex populations from 11 reservoirs, habitats characterized by longitudinal gradients in abiotic and biotic conditions. We hypothesized that sites with different environmental conditions should have divergent infection patterns. We sampled three stations along each reservoir (upstream, middle and downstream) in the summer and autumn of 2 years. Four groups of parasites were analysed for their spatial variation: the protozoan Caullerya mesnili, the yeast Metschnikowia sp., microsporidia and oomycetes. The microsporidia were evenly distributed between seasons, as well as among-and within-reservoirs. In contrast, C. mesnili and Metschnikowia sp. were more prevalent in autumn than in summer, whereas the prevalence of oomycetes was higher in summer. On a within-reservoir scale, C. mesnili was significantly more prevalent in upstream parts of the reservoirs, whereas Metschnikowia sp. and oomycetes were more prevalent in the central and downstream areas. In summary, the within-reservoir distribution of certain Daphnia parasites seems to be affected by environmental gradients (most probably food abundance and predation pressure). Thus, environmental heterogeneity should be considered in future studies of host-parasite interactions, even on a local scale.