The city of Makassar is located in Maros, Tabaringan, Tallo, Jeneberang and Gowa-Takalar watersheds and Makassar non-watershed areas.This area is located along the coast of Makassar City whose stream flow is directly mainly to the sea or through small rivers (creek ). For the calculation of flood discharge, the study of watershed becomes crucial to know the position of study area to the influence of upstream river basin. Watershed area is very influential to flood discharge.In general, the larger the watershed the greater the amount of surface runoff is so that the greater the flow of surface or flood discharge. This study aims to identify the watershed and its effect towards floods in Makassar. By using an integrated spatial analysis method in Geographic Information Systems (SIG) version 10.5 application, the watershed of Makassar can be identified. The results show that watershed in Jeneberang region is the largest watershed area that empties into Makassar City. The watershed reaches 76,085.06 hectares while the Gowa-Takalar watershed is the smallest of 1.88 hectares. There are 2 watershed areas that have no effect on the risk of flood in Makassar City namely Maros watershed and Gowa-Takalar watershed. The research results can be utilized for water resource management needs such as primary and secondary flow planning, both by practitioners and the government of Makassar City.