This investigation targeted the largest morphologically complex reservoir (Soyang) in South Korea during 1992–2013. It is a prominent source of domestic water supply, irrigation, flood control, and hydroelectric power generation. Therefore, this investigation focused on regional- to global-scale applications. We revealed the empirical links between chlorophyll (Chl-a) and total nitrogen (TN) and total phosphorus (TP), the impact of the monsoon regime on nutrients, and flood and drought regime. Further, we investigated the trophic status dynamics, tendencies of water chemistry factors, and valuation of zonal water chemistry by the application of a modified multimetric water pollution index (WPI). The physicochemical indicators illustrated significant disparities among the Lacustrine (Lz), Transition (Tz), and Riverine (Rz) zones. The solid contents (TSS) displayed a significant increase in the lake zones in the order of Lz (4.58 ± 13.7 mg/L), Tz (6.16 ± 16.2 mg/L), and Rz (7.38 ± 18.9 mg/L). However, TP and allied chemical species revealed an inverse relationship with the TN:TP ambient ratios. Nevertheless, Chl-a displayed sharp interzonal fluctuations from the Lz (2.90 ± 3.29 µg/L) to Tz (4.61 ± 4.98 µg/L). The seasonal deviations, however, exposed divergent heterogeneities among the TSS, TN, TP, and Chl-a. The regression plot between the observed and predicted Chl-a in the Soyang reservoir displayed a very strong relationship (R2 = 0.997). The seasonal and interannual variations of trophic status displayed a higher impact of precipitation, particularly in the case of TP and Chl-a. The flood years indicated phosphorus limitations, while drought years alluded to the non-algal light limitations (biogenic turbidity). Water temperature (WT), dissolved oxygen (DO), biological oxygen demand (BOD), TSS, TP, and Chl-a displayed decreasing trends in the ambient water. In contrast, pH, chemical oxygen demand (COD), electrical conductivity (EC), and TN displayed increasing tendencies by the application Mann–Kendall trend analysis. The WPI outcomes designated Lz with excellent water quality while Tz an Rz indicated good water quality. It also indicated impending sedimentation tendencies in the Rz. In conclusion, our findings indicated fluctuating rainfall patterns (drought and flood conditions) that significantly impacted the Soyang reservoir water quality, flood and drought severity, and trophic status of the reservoir. This study highlights the requirements of further studies to substantiate the drought and flood dynamics and their impacts on nutrients and overall water quality status.