We present a time series of 13 years (2003–2016) of continuous monthly data on the prevalence and mean abundance of the trematode Oligogonotylus mayae for all the hosts involved in its life cycle. We aimed to determine whether annual (or longer than annual) environmental fluctuations affect these infection parameters of O. mayae in its intermediate snail host Pyrgophorus coronatus, and its second and definitive fish host Mayaheros urophthalmus from the Celestun tropical coastal lagoon, Yucatan, Mexico. Fourier time series analysis was used to identify infection peaks over time, and cross-correlation among environmental forcings and infection parameters. Our results suggest that the transmission of O. mayae in all its hosts was influenced by the annual patterns of temperature, salinity and rainfall. However, there was a biannual accumulation of metacercarial stages of O. mayae in M. urophthalmus, apparently associated with the temporal range of the El Niño-Southern Oscillation (five years) and the recovery of the trematode population after a devasting hurricane. Taking O. mayae as an example of what could be happening to other trematodes, it is becoming clear that environmental forcings acting at long-term temporal scales affect the population dynamics of these parasites.