The importance of parasites as both members of biological communities and as structuring agents of host communities has been increasingly emphasized. Yet parasites of aquatic macroinvertebrates and the environmental factors regulating their richness and abundance remain poorly studied. Here we quantified parasite richness and abundance within 12 genera of odonate naiads and opportunistically sampled four additional orders of aquatic macroinvertebrates from 35 freshwater ponds in the San Francisco Bay Area of California, USA. We also tested the relative contributions of host- and habitat-level factors in driving patterns of infection abundance for the most commonly encountered parasite (the trematode Haematoloechus sp.) in nymphal damselflies and dragonflies using hierarchical generalized linear mixed models. Over the course of two years, we quantified the presence and intensity of parasites from 1,612 individuals. We identified six parasite taxa: two digenetic trematodes, one larval nematode, one larval acanthocephalan, one gregarine, and a mite, for which the highest infection prevalence (39%) occurred in the damselfly genus, Ishnura sp. Based on the hierarchical analysis of Haematoloechus sp. occurrence, infection prevalence and abundance were associated predominantly with site-level factors, including definitive host (frog) presence, nymphal odonate density, water pH and conductivity. In addition, host suborder interacted with the presence of fishes, such that damselflies had higher infection rates in sites with fish relative to those without, whereas the opposite was true for dragonfly nymphs. These findings offer insights into the potential interaction between host- and site-level factors in shaping parasite populations within macroinvertebrate taxa.