As environmental change drives reductions in free-living species abundance and diversity, at least two alternative pathways are possible for parasitic species. On one hand, diversity losses could drive parasite population declines or extirpations, with potentially influential effects on ecosystem processes, given parasites' ecological importance. On the other hand, host species loss could reduce the abundance of non-competent hosts that interfere with pathogen transmission or facilitate increases in the abundance of “weedy”, highly competent host species, intensifying transmission. While many experimental studies have investigated how changes in free-living species affect the fate of individual parasite species, comparatively little is known about the consequences across multiple parasite taxa within an ecosystem, limiting opportunities to assess the proportion of species that are likely to take each of the alternative pathways. Here, we present results of a before-after-control-impact (BACI) experiment conducted in central California, USA, in which we manipulated bird activity at the scale of wetland ecosystems and tracked the resulting effects on the identity and abundance of protozoan and metazoan parasites of amphibians. Of the eight common parasite taxa that constituted ~97% of parasite observations, four responded negatively to bird-augmentation treatments, two responded positively, and two exhibited no significant response. We conclude that it is possible, within a single ecosystem, for free-living species change to produce declines in some parasite species, increases in others, and no change in yet other species. Disease ecology urgently needs tools for forecasting when and where each of these effects should occur, which will facilitate management efforts focused on mitigating outbreaks of disease on one hand and preventing extinction of parasite species on the other.