This research aimed to identify water quality changes in the Cirata Reservoir and the factors affecting them in terms of hydrology and climate. The sampling was carried out in both the rainy and dry seasons at 12 locations in the Cirata Reservoir. The Mann–Whitney U-test (different test) results showed that salinity, total suspended solids (TSS), the potential of hydrogen (pH), nitrate (NO3-N), phosphate (PO4), nitrate and phosphate content in the sediment were significantly different (α < 0.05) between the rainy and dry seasons. The principal component analysis (PCA) results showed that the water quality characteristics in the Cirata Reservoir in the dry season were influenced by environmental conditions in the reservoir, especially by the floating cage aquaculture and climate conditions. The high solar radiation, low rainfall, and floating cage aquaculture increased the pH and amounts of dissolved oxygen (DO), ammonia (NH3-N), PO4, nitrate and phosphate in the sediment while decreasing transparency, salinity, TSS, and NH3-N. During the rainy season, the high runoff from Citarum Watershed controlled the water quality characteristics of the Cirata Reservoir. In this season, transparency, salinity, pH, DO, NH3-N, PO4, nitrate and phosphate in the sediment increased, while TSS tended to be low. In general, the water volume addition decreased the nutrition and salinity concentration in the water body. However, a distinct phenomenon occurred in the Cirata Reservoir. The runoff from agriculture, settlement, livestock, and the Citatah Karst in the Upper Citarum Watershed increased nutrition and salinity in the reservoir. Land use in the Citarum Watershed and floating cage aquaculture had an important role in the reservoir water quality.