AbstractThis paper presents a stochastic procedure for the solution of groundwater flow through a random shallow semiconfined aquifer. Problems dealing with flow through a semiconfined aquifer with multiple random parameters subject to deterministic boundary conditions and domain recharge are investigated using perturbation techniques associated with boundary element methods. Both the transmissivity of the main aquifer and the resistance of the leaky layer are considered as random parameters. The perturbation boundary element method does not require specification of the probability density function of the parameters but only their expectations, variances and the covariance of the two parameters. To illustrate the applicability of the method, three simple numerical examples are presented. A one‐dimensional example is examined and compared with the exact solution, along with the perturbation solutions for two two‐dimensional flow problems.