Centrocestus formosanus is a digenetic trematode from Asia that parasitizes multiple hosts and is a concern in the Comal River, Texas, USA, because of its negative effects on the endangered fountain darter Etheostoma fonticola. To determine a practical sampling method to monitor C. formosanus in the Comal River, we evaluated three sampling methods using wild-caught fish, caged fish reared in the laboratory, and cercariometry. Cercariometry detected significant spatial and temporal patterns of cercarial density in river water that were similar with metacercarial intensity in caged fish, but inconsistent with metacercarial intensity in wild-caught fish. Our results also showed a positive correlation between cercarial density in river water and metacercarial intensity in caged fish. Conversely, the relationship was not significant between cercarial density and metacercarial intensity in wild-caught fish. Because cercariometry predicted similar trends with the caged fountain darter sampling method, cercariometry was useful in predicting C. formosanus gill infections, infection rate, and longevity in infected fountain darters. Although trends from cercariometry and caged fish sampling methods were similar, we recommend cercariometry because it was less expensive to use given the amount of sampling effort required and provides trends that can be used to make pro-active management decisions in C. formosanus-infested aquatic ecosystems.