The dyke system plays a vital role in cultivating rice intensively in the Vietnamese Mekong Delta, which protects rice paddy fields from annual floods. This study aimed to examine whether the full-dyke system (FD, which restricts water exchange for a long time) can cause degradation of surface water quality and reduction in benthic invertebrate biodiversity. The surface water quality and benthic invertebrate community were compared between the FD and semi-dyke systems (SD, which permits water exchange during flooding season) using a large number of samples collected seasonally in 2019. The results showed that the surface water quality within the FD system had significantly higher concentrations of TSS, COD, BOD5, N-NO3⁻, N-TKN, P-PO4³⁻, and TP than compared to the SD system (p < 0.05), indicating greater pollution levels. The benthic invertebrate community was less diverse in the FD system than in the SD system. Only 17 species (belonging to 4 families) were detected in the FD system, and 30 species (belonging to 5 families) were detected in the SD system. The benthic invertebrate community structure changes and biodiversity loss were associated with degraded water quality. The P-PO4³⁻ and TP parameters were negatively correlated with the number of species, density, and biomass in the FD system and with the Shannon–Wiener (H′) index in the SD system. In conclusion, the FD system has been degrading water quality and causing biodiversity loss.