This study was performed to determine the ecological health of a temperate river over nine years (2011–2019); it also analyzed the trophic structure and linkage of nutrients (nitrogen [N] and phosphorus [P]), sestonic chlorophyll-a (CHL-a), and the top trophic fish in the Asian monsoon region. Water chemistry, trophic indicators, and tolerance guilds were primarily influenced by land use and land cover (LULC); the magnitude of variation was also related to geographic elevation, artificial physical barriers (weirs), and point sources. Levels of nutrients, organic matter, and CHL-a largely influenced by the intensity of the monsoon seasonality for a particular LULC and stream order. Mann–Kendall tests based on a long-term annual dataset showed that annual organic matter and CHL-a increased over time because of longer hydraulic residence time after weir construction. The results of empirical nutrient models suggested that P was the key determinant for algal growth (CHL-a); the strong P-limitation was supported by N:P ratios > 17 in ambient waters. Linear regression models and canonical correspondence analysis (CCA) were used to determine the influences of LULC and water quality on the trophic/tolerance linkages, fish community compositions and structures, and river health. Tolerant species had a positive functional relationship with nutrient enrichment through total phosphorus (TP) (R2 = 0.55, p < 0.05) and total nitrogen (TN) (R2 = 0.57, p < 0.05), organic pollution in terms of biological oxygen demand (BOD) (R2 = 0.41, p < 0.05) and chemical oxygen demand (COD) (R2 = 0.49, p < 0.05), and algal growth (R2 = 0.47, p < 0.05); sensitive species exhibited the opposite pattern. The degradation of river health, based on the multi-metric index of biotic integrity (IBI) model, was evident in the downriver region (“fair–poor” condition) and was supported by the quantitative fish community index (QFCI) model. The outcomes suggested that the degradation and variation of ecological river health, trophic linkages of water chemistry (N, P)-algal biomass-fish, were largely controlled by the land use pattern and construction of physical barriers in relation to the Asian monsoon.