Quantifying the hydrologic response of land use/land cover change (LULCC) is of paramount importance to improve land management. This study was carried out to analyze the effect of LULCC on water quality and quantity. LULCC of the watershed in 1986, 1999 and 2011 was analyzed from Landsat satellite images using supervised classification. Time series and point data were collected from the upper and lower sections of Wedesa, Wesha and Hallo Rivers. Water quality parameters (turbidity, suspended solid (SS), total dissolved solid (TDS), pH, electric conductivity (EC), total organic carbon (TOC), ammonia, nitrate and phosphate) were analyzed in the laboratory. A considerable decline in forest and an increase in woodland were observed in the watershed during the indicated periods. Turbidity, SS, TDS and EC were significantly higher (P < 0.05) in the lower section of the rivers compared to the upper ones. Ammonia, nitrate and phosphate were higher in the lower section of some rivers compared to the upper ones. In general, water quality in the upper watershed of the three rivers was better than the lower one with respect to considered parameters, which might be related to the observed LULCC. Most water quality parameters varied (P < 0.05) seasonally in both the upper and lower sections of the rivers. Despite the irregular rainfall pattern and increased water consumption from the catchment, the annual discharge of the Tikur-Wuha River to Lake Hawassa shows an increasing trend. We concluded that the discharge is not only related to the upstream LULCC but also to the management of the Cheleleka wetland. However, further investigation is required to determine the dominant factors affecting inflow discharge to Lake Hawassa.