This study was conducted to assess the water quality affected by different land use patterns in U Minh Ha National Park, Ca Mau, Vietnam. This study determined the water quality characteristics in three land use types (Acacia hybrid, planted melaleuca cajuputi, and natural melaleuca cajuputi) at different plant ages on two acid sulfate soil layers in the rainy season (8/2018) and dry season (4/2019) using nine water quality parameters. Multivariate statistical analyses were applied to evaluate the correlation and spatial and temporal variations in the water quality. The study results showed that the water quality in S-ASS was more polluted than that in D-ASS, characterized by low pH; the EC, organic matters (BOD and COD), nutrients (N-NH4+ and N-NO3−), and metal ions (Al3+ and Fe3+) were high; and the EC, BOD, COD, Al3+, and N-NO3− were determined high in D-ASS. The NMC area was noted to have high concentrations of organic matters and nutrients, while the factors specific to acidic soil were found to be higher in the AH and PMC areas. The water quality in the rainy season tended to be more polluted than that in the dry season. The cluster analysis grouped the land use patterns on S-ASS and D-ASS in both seasons into four groups, with a clear similarity between the wet and dry seasons in the areas at various plant ages. The seasonal variations of the water quality of the three land use types were distinguished by the main parameters, including pH, EC, BOD, N-NO3−, and Al3+ (S-ASS) and EC, BOD, N-NO3−, N-NH4+, and Fe3+ (D-ASS). Therefore, there is a need for better water management measures in the rainy season and focus on the key parameters causing water quality variations in each area. The findings in this study provided important information for the future water quality monitoring for both agricultural production and conservation in the national park.