AbstractPopulations of stream organisms often show large heterogeneity in space, which can substantially influence community dynamics and ecosystem functioning. However, few studies have examined spatial heterogeneity of parasites in lotic ecosystems, especially at fine spatial scales (e.g., within stream reaches).We quantified parasite infections in 3,255 host snails (Juga plicifera) at 1‐m intervals along three second‐order stream reaches to examine relationships between trematode parasite infections, fine‐scale heterogeneity in host characteristics (density and size), and the stream environment (depth, allochthonous materials, flow velocity, and substrate rugosity). We then conducted a field experiment to specifically test the effect of resource heterogeneity in the form of leaf litter on trematode densities (i.e., infected snails per unit area), which represents a measure of local disease risk to secondary hosts. We hypothesised that variation in bottom‐up effects of host resources to snail hosts to parasites would drive spatial heterogeneity in trematode density.In the field surveys, trematode density ranged from 0 to 80 infected snails/m2 and showed spatial autocorrelation within two of three stream reaches. Trematode density increased with snail density, which was positively related with the amount of allochthonous materials but negatively related to steam depth. Individual host infection probability increased with snail size, which was positively related to both allochthonous materials and stream depth.In the experiment, host snail and trematode densities increased by 3‐fold and 4‐fold, respectively, in the leaf addition treatments relative to controls. The experiment therefore provided mechanistic understanding of patterns from the surveys by demonstrating a bottom‐up effect from high quality resources to host space use to trematode density.Our results demonstrate a strong role of within‐reach variation in allochthonous resources and habitat (depth) in driving spatial heterogeneity of stream parasites, which probably creates fine‐scale hotspots of disease transmission to downstream hosts. More broadly, our findings help integrate parasites into our understanding of how environmental heterogeneity influences community structure and ecosystem processes (e.g., disease risk) in streams.