Understanding the distinct hydro-biogeochemical dynamics of lotic and lentic systems is crucial for integrated watershed management, particularly in regions with complex land-use patterns. This study investigated the spatiotemporal water quality variations in Gunsan City, Republic of Korea. Monthly monitoring was conducted at 17 sites (8 rivers and 9 reservoirs) from May 2024 to May 2025 to analyze 11 physicochemical parameters. Multivariate statistical approaches, including Factor Analysis of Mixed Data and K-means clustering, were employed to elucidate the interactions between water body types and seasonal factors. Factor analysis identified two primary gradients explaining 42.7% of the total variance: anthropogenic nutrient loading (Axis 1) and seasonal metabolic-physical drivers (Axis 2). The study revealed distinct spatial heterogeneity; rivers exhibited significantly higher electrical conductivity and nutrient concentrations (e.g., TN, TP) compared to reservoirs, clustering into a high-pollution group driven by point and non-point sources. Seasonally, rivers showed a marked concentration effect during the dry winter season due to reduced base flow, whereas reservoirs maintained relatively stable water quality attributed to the dilution capacity of larger water volumes. Shallow reservoirs like Backseokje exhibited characteristic water quality pattern, such as hypoxia related to organic matter decomposition and high vegetation cover. These findings suggest that a differentiated management approach is essential: mitigating point-source and non-point-source pollution and securing base flow for rivers during dry seasons, while regulating internal biogeochemical processes and inflows for reservoirs.