BACKGROUND: As habitat fragmentation increases, ecological processes, including patterns of vector-borne pathogen prevalence, will likely be disrupted, but ongoing investigations are necessary to examine this relationship. Here, we report the differences in the prevalence of Lyme disease (Borrelia burgdorferi sensu lato, s.l.) and haemoproteosis (Haemoproteus spp.) pathogens in avian populations of a fragmented habitat. B. burgdorferi s.l. is a generalist pathogen that is transmitted by Ixodes pacificus vectors in California, and Haemoproteus is an avian parasite transmitted by Culicoides vectors. METHODS: To determine whether biotic (avian and mammalian abundance) or abiotic characteristics (patch size and water availability) correlated with infection prevalence change, we screened 176 birds sampled across seven sites in oak woodland habitat in northern California. RESULTS: While biotic factors correlated with an increase in both pathogens, infection prevalence of Haemoproteus spp. was only associated with individual-level traits, specifically foraging substrate and diet, and B. burgdorferi s.l. was associated with community-level characteristics, both total mammal and, specifically, rodent abundance. Proximity to water was the only abiotic factor found to be significant for both pathogens and reinforces the importance of water availability for transmission cycles. Larger patch sizes did not significantly affect infection prevalence of Haemoproteus, but did increase the prevalence of B. burgdorferi. CONCLUSIONS: These results highlight that while environmental factors (specifically habitat fragmentation) have a limited role in vector-borne pathogen prevalence, the indirect impact to biotic factors (community composition) can have consequences for both Haemoproteus and B. burgdorferi prevalence in birds. Given the pervasiveness of habitat fragmentation, our results are of broad significance.