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Karachi, the biggest city of Pakistan, has undergone various urban sprawls due to its continuously growing population that has severely affected its natural drainage pattern. The city had an extensive natural drainage system which has now lost its original form. This study investigated the blockages and their causes during the last two decades in one of the city's riverbeds-Malir. Moreover, the extent of floods identifying the vulnerability of the watershed's urban area after major rainfall events was modeled. The geospatial techniques and satellite images of Landsat 5, 7, and 8 were used to analyze the changes in land use and land cover (LULC) of the Malir Basin. The Shuttle Radar Topographic Mission (SRTM) Digital Elevation Model and topographic sheets of 1975 were utilized to delineate the natural drainage network and streambeds of the basin using geographical information system (GIS) tools. Historical rainfall data from 1985 to 2014 were acquired from the Pakistan Meteorological Department (PMD) to simulate runoff using the US Hydrologic Engineering Center's Hydrologic Modeling System (HEC-HMS and HEC-GeoHMS). The flood modeling was done using the River Analysis System (HEC-RAS and GeoRAS). Rainfall-runoff simulations and flood extent and depth of five major rainfall events-1992, 2003, 2007, 2009, and 2013-were modeled in this study. GIS overlay analysis combined the LULC, riverbed, and drainage line layers to identify the blocked area and to quantify the specific LULCs that were causing blockages in the riverbed. Several maps, which are prepared in this study, show the parts of the river with altered drainage patterns in 2013 from what existed back in 1975.