A seasonal investigation on the occurrence of fishborne zoonotic trematodes (FZT) in economically important mono-cultured hybrid catfish and giant gouramy was conducted in the Mekong Delta of Vietnam. Fish from carp poly-culture and intensive small-scale integrated vegetable–aquaculture–animal husbandry farming (VAC) systems were also examined. No FZT metacercariae were found in any mono-cultured hybrid catfish. FZT metacercariae were common, however, in fish from the other three systems: All metacercariae belonged to the Heterophyidae family of trematodes, Haplorchis pumilio, H. taichui, Centrocestus formosanus and Stellantchasmus falcatus. The FZT prevalence was 1.7% in mono-cultured giant gouramy, 6.6% in carp from the poly-culture and 3.0% in fish raised in the VAC system. H. pumilio was the most common FZT species constituting more than 58.0% of all metacercariae recovered. The prevalence of infection was significantly higher in the flooding season compared to the non-flooding season for both giant gouramy and fish reared in the VAC system. FZT intensity was greatest in fish from carp poly-culture, particularly in the flooding season. The results indicate that certain fish production systems are at risk for FZT, and control approaches will benefit from understanding these risk factors.