This study was conducted in the Lake Hawassa System as examprarily case for heavily contaminated surface water systems in emerging economies with scarce data and need for elucidation of sources to derive targeted and cost-effective mitigation measures. Water quality parameters were measured at 25 stations along with flow measurements and the use of SWAT for flow simulation. Two water quality indices were used to assess the suitability of water for anthropogenic uses. The trophic status of Lake Hawassa was determined using Carlson TSI.