Deterioration of coastal water quality is a significant concern in economically active cities in South Korea. In response, the South Korean government initiated the total pollutant load management (TPLM) program to control pollutant levels. However, the current evaluation method, based on pre-post comparison, may lead to a biased estimate. Thus, this study aims to establish a cause-and-effect relationship between the TPLM program and coastal water quality improvement using a dataset of over 15,000 observations from 2011 to 2021. A difference-in-difference model was employed to assess the program’s impact, considering its staggered implementation and changes in evaluation frequency. Although the effects on overall treated regions remain inconclusive, the study found evidence of water quality improvement associated with changes in evaluation frequency. For instance, chemical oxygen demand levels decreased by 4.8% to 9.8% points, and total phosphorus levels decreased by 11.5% to 14.8% points, maintaining consistency across robustness checks. These findings suggest that frequent municipal evaluations are effective in managing emission reductions. Therefore, it is recommended that the South Korean government, which currently conducts quarterly water quality tests, increase the evaluation frequency for improved monitoring and better control of non-point sources.