The stochastic process of container loading is described in the paper with special emphasis to ship motion when she is lying at a quay. The 3 DOF system was applied to describe rolling, pitching and heaving of a vessel which may cause a significant variations of momentary deck elevation. The realistic range of such variations are assessed for a variety of cargo locations on-board and a phase shift between two independent gantries engaged in cargo operations. The process is modeled with regard to random character of crucial variables affecting ship motion due to cargo loading.