A method is described for the computation of the two-dimensional unsteady motion of a solitary wave passing over submerged breakwaters. Far from the breakwater the fluid is assumed static and the sea bed is level. The fluid motion is assumed to be irrotational, incompressible and inviscid. The exact boundary conditions at the free surface and the impermeable bed are satisfied. Laplace's equation for the velocity potential is solved using a boundary integral method. Numerical results are reported which show the variety of ways in which solitary waves are distorted when they encounter submerged breakwaters.