Water quality degradation is one of the major problems with artificial lakes in estuaries. Long-term spatiotemporal patterns of water quality in a South Korean estuarine reservoir were analyzed using seasonal datasets from 2002 to 2020, and some functional changes in relations of trophic state variables due to the construction of serial weirs in the upper river were also investigated. A total of 19 water quality parameters were used for the study, including indicators of organic matter, nutrients, suspended solids, water clarity, and fecal pollution. In addition, chlorophyll-a (CHL-a) was used to assess algal biomass. An empirical regression model, trophic state index deviation (TSID), and principal component analysis (PCA) were applied. Longitudinal fluctuations in nutrients, organic matter, sestonic CHL-a, and suspended solids were found along the axis of the riverine (Rz), transition (Tz), and lacustrine zones (Lz). The degradation of water quality was seasonally caused by resuspension of sediments, monsoon input due to rainfall inflow, and intensity of Asian monsoon, and was also related to intensive anthropic activities within the catchment. The empirical model and PCA showed that light availability was directly controlled by non-algal turbidity, which was a more important regulator of CHL-a than total nitrogen (TN) and total phosphorus (TP). The TSID supported our hypothesis on the non-algal turbidity. We also found that the construction of serial upper weirs influenced nutrient regime, TSS, CHL-a level, and trophic state in the estuarine reservoir, resulting in lower TP and TN but high CHL-a and high TN/TP ratios. The proportions of both dissolved color clay particles and blue-green algae in the TSID additionally increased. Overall, the long-term patterns of nutrients, suspended solids, and algal biomass changed due to seasonal runoff, turnover time, and reservoir zones along with anthropic impacts of the upper weir constructions, resulting in changes in trophic state variables and their mutual relations in the estuarine reservoir.