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Based on random theory,fluid dynamics,porous media and soil mechanics,the porosity and random characteristic of the two-layer soft soil in Wuhan region were studied in this paper.The random seepage coefficient on the two-layer soft soil was analyzed,and the seepage model and its random distribution function were given.The groundwater flow differential equations related to the two layer soft soil structure were also established.The evaluation procedure of effect boundary on the pumping water in deep foundation pit was put forward.Moreover,with an engineering example,the probability distribution on random boundary prediction for pumping water of foundation pit was computed.