The dynamics of vector-borne parasites are driven by interactions between factors intrinsic to the parasite, its host, as well as environmental fluctuations. Understanding these interactions requires a long-term view, especially to predict the consequences of climate change on parasite dynamics.The goal of this study is to evaluate temporal fluctuations in individual probability of infection, its environmental drivers and consequences for host body condition, of three malaria parasites (Plasmodium azurophilum, P. leucocytica, and P. floridense) infecting the lizard, Anolis gundlachi, in the rainforest of Puerto Rico.We conducted 13 surveys totaling N > 8000 lizards over 26 years. During the early years of the study, the lizard’s probability of infection by all three Plasmodium species appeared stable despite disturbances from short droughts and small to moderate hurricanes.Over a longer timescale, we found that the individual lizard probability of infection and overall prevalence varied significantly over the years, and this fluctuation was driven in non-linear ways by variations in temperature and rainfall. The probability of infection was maximized at intermediate levels of temperature and precipitation. This temporal variability in Plasmodium prevalence driven by environmental factors had two important consequences. First, temperature-mediated a decrease in body condition in infected female lizards relative to non-infected ones. Second, Plasmodium parasite species composition varied through time.Overall, the results show how environmental conditions, such a severe drought, can drive disease dynamics outside of their apparent stable equilibrium and mediate the potential negative effects of parasite infection on the host. Our results also emphasize the need for long-term studies to reveal host-parasite dynamics, their drivers and consequences.