To investigate the factors affecting water quality in coastal regions with sea dike constructions, surface water outside a sea dike was monitored for six years from 2015 to 2020 in the Saemangeum region of Korea. Statistical analyses of the six years of high-frequency measurements revealed that the water quality in this system was predominantly governed by natural processes followed by pollutant inputs as the secondary influencing factor. Severe dissolved oxygen (DO) depletion was observed in the surface waters during warm periods, probably owing to the advection of DO-depleted water from elsewhere to the surface layer. Based on the apparent oxygen utilization (AOU)–pH relationship (r = 0.52, n = 1837), the maximum AOU (180 µM) led to a pH decrease from 8.04 to 7.50, which was considerably lower than the estimated value of 7.72. This extra pH drop was probably due to a reduction in the buffering capacity associated with increased CO2 in the water column originating from the atmosphere and in situ production, as well as local water column redox reactions associated with benthic inputs of reduced chemical species. Overall, persistent DO depletion with ongoing eutrophication/hypoxia could accelerate ocean acidification in Korean coastal waters, which could be more acute in coastal regions with artificial coastal constructions.