The Special Region of Yogyakarta is one of the regions experiencing population growth every year. With the increase in the number of settlements and the reduction of open land, it will affect the hydrological conditions of one of the rivers that passes through the city of Yogyakarta, namely the Winongo River. This causes the vulnerability of flooding in the Yogyakarta Region by changing the recharge area into a non-recharge area (run off). The purpose of this study is to examine the impact of land use changes on flood vulnerability in the Yogyakarta area. The method used in assessing the impact of changes in land use on flooding using the Soil & Water Assessment Tools (SWAT), ArcSWAT and with the help of Geographic Information System (GIS) in processing spatial data. Land use data used are 2016 land use maps and 2016 land use scenarios by replacing rice fields in the upstream and downstream areas into residential land. The results of this study indicate that by changing the recharge area to non-absorption by 20.6 % causing an increase in flood discharge of 115.5 m3 / s or 1.47 %.