The Code River is a river located in the Special Province of Yogyakarta (DIY) and one of the rivers that divide the City of Yogyakarta. There are three regency regions crossed by the Code River, specifically: Sleman Regency, Yogyakarta City and Bantul Regency. The majority of the people around the river use the river as the needs of MCK (bath, wash and toilet), irrigation water for agriculture and plantations, industrial runoff / hotel waste and sand mining. Utilization of the river will be caused a decrease in the level of river water quality and erosion on the surface which is then carried by the flow in the form of sediment granules (Sediment Transport). The purpose of this study was to determine the level of water quality and the amount of sediment transport that occurred at three points of the Code River. To find out its purpose, this study will uses the Water Quality Index method - National Sanitation Foundation (IKA - NSF) and empirical formula with the Meyer – Peter Muller and Frijlink methods in the calculations. Based on the results of research at the three review locations on Code River for quality analysis water using the IKA – NSF method, show the level of river water quality has decreased, so that the status is moderate – bad with a range of 43 – 51. Whereas, for the analysis of the amount of sediment tranport theere was also a decrease in the MPM method, the results obtained were equal to Tb 1 = 96,457 m3/day, Tb 2 = 32,853 m3/day, Tb 3 = 19,898 m3/day and the Frijlink method obtained that was equal to Tb 1 = 36,21 m3/day, Tb 2 = 24,697 m3/day, Tb 3 = 11,862 m3/day.