A survey for fish-borne zoonotic trematode (FZT) metacercariae in fish from the Northern Mountain Region of Vietnam was conducted from May to August 2014. The major objective was to evaluate the impact of water body types on the prevalence of FZT. A total of 846 fish (31 species) were collected from three water body types, including aquaculture ponds, rivers, and reservoirs. A pepsin digestion method was used for the recovery of metacercariae from fish. Overall, 29 of the 31 fish species were infected with FZTs. Prevalence was 56.8% in river fish, 46.7% in pond fish, and 29.3% in reservoir fish. The prevalence of Clonorchis sinensis metacercariae was 10.6% in reservoir fish, and 2.6% in river fish; fish from ponds were uninfected. The infection intensity of C. sinensis was 29.7 metacercariae/reservoir fish and 2.1 metacercariae/river fish. The prevalence of C. sinensis was highest (25.9%) in Toxabramis houdemeri. The intestinal flukes Haplorchis pumilio, Haplorchis taichui, Haplorchis yokogawai, Centrocestus formosanus and Procerovum varium were recovered from 29 fish species, with an overall prevalence of 46.8% and a mean infection intensity of 23.6 metacercariae. The results indicate that a C. sinensis sylvatic cycle involving wild fish species is important in the epidemiology of liver fluke and that consumption of raw or inadequately prepared wild-caught fish is a the major risk factor for human Clonorchiasis in this region. Both wild-caught and cultured fish present a high risk for infection with intestinal flukes. The habitat requirements of the snail host may be the important determining factor in favoring a sylvatic cycle of C. sinensis. This information is relevant to the development of effective prevention and control strategies, and emphasizes the priority that must be given to education of the local communities on the risks of consuming raw or improperly prepared fish dishes.