Flash floods are considered natural disasters that can cause casualties and demolishing of infrastructures. The flash flood takes place over Abu Rusheid in 29 November 2011. After one month from the falling of flood, ten flooding water samples were collected from the cavities in the mountain at Abu Rusheid area, South Eastern Desert, Egypt. The salinity ranges between 380 and 1460 ppm, while pH ranges between 7.1 and 8.1. Trioctyl amine (TOA) dissolved in kerosene has been chosen for removal both of uranium and thorium. Different parameters were carried out testing the following variables: different diluents, TOA concentrations, aqueous to organic phase ratio, shaking time, temperature, and different stripping agents. The factors studied were followed by application of the removal system to determine the uranium and thorium from flooding water samples. The uranium concentration in the studied area were ranged between 172 ppb and 1012 ppb. While, thorium was ranged between 98 ppb and 524 ppb. Meanwhile, the dissolution and leaching (%) of uranium and thorium in flood water samples after one month from the falling of flood in the studied area are ranging between 0.032-0.9 % and 0.016-0.36 %. After chemical treatment of the flood water was observed that, the remaining elements of uranium and thorium are very few. We recommend not to use those waters from flooding which contain a small concentration of uranium.