The expansion of the mode composition and amplification of long-wave oscillations in systems of adjacent bays due to their coupling through entrances can make a serious threat to the operation of ports and their coastal infrastructure. Based on the nonlinear numerical model FUNWAVE (fully nonlinear WAVE model), seiche oscillations in a system of two adjacent model bays of different sizes, excited by the action of a soliton, were studied. It was found that the large bay A has a significant effect on oscillations in the adjacent smaller bay B, in which, due to the coupling, an intense oscillation with a period corresponding to the Helmholtz mode of bay A is generated, dominating over all other eigenmodes. The condition under which the Helmholtz mode of bay A does not penetrate into bay B was obtained. Higher frequency eigenmodes are also excited in the bays under consideration. Their intensity is low and weakly depends on the distance between the bays.