Madukismo Sugar Factory dispose their waste into the river. The river water which is polluted by the waste, infiltrate into the ground and so the ground water undergo the physical changes such as smells and colour. This study aims to investigate the quality of COD in wells water and assess the impacts that may arise as a result of waste disposal from Madukismo Sugar Factory. The method used in this research is based from SNI 6989.2.2009 about COD test with closed reflux in spectrophotometry. Samples will be taken as many as twenty samples consisting of ten sample in the morning and ten sample in the  afternoon. GIS is used to further clarify the location of sampling points that have been determined.. After investigation, COD concentration in the morning is smaller than the COD concentration in the afternoon. The highest concentration of COD in the morning was found in Well H with 66,88 mg/L. While the smallest concentration of COD in the mornng was found in Well D with 36,8 mg/L. The highest concentration of COD in the afternoon was found in Well A with 72,50 mg/L. The smallest concentration of COD in the afternoon was found in Well D and J with 53,13 mg/L. The distance of wells water also affecting the concentration of COD. Closer the wells water with madukismo  sugar factory, the concentration of COD will be higher. After investigation, its known that the groundwater around the Madukismo Sugar Factory was polluted by COD. The concentration of COD in wells water was exceeded the quality standard based on Yogyakarta Governor Regulation No.20 of 2008. After analyzing the impact of COD for human health, COD didnt have an immediate impact for human health. For waste treatment, the researcher recommended to using  Constructed Wetland with Cattail plant 
Keywords : COD, GIS, groundwater, sugar factory’s waste, wells water