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A stochastic model was developed to simulate the flow in heterogeneous media subject to random boundary conditions.Approximate partial differential equations were derived based on the Karhunen-Loeve (KL) expansion and perturbation expansion. The effect of random boundary conditions on the two-dimensional flow was examined. It is shown that the proposed stochastic model is efficient to include the random boundary conditions. The random boundaries lead to the increase of head variance and velocity variance. The influence of the random boundary conditions on head uncertainty is exerted over the whole simulated region, while the randomness of the boundary conditions leads to the increase of the velocity variance in the vicinity of boundaries.