Based on our previously proposed modified Monte Carlo method, which is efficient to simulate the time-dependent polarized radiative transfer problem in an atmosphere-ocean model with a reflective/refractive interface, we further investigate the square pulse effect on the polarized radiative transfer in an atmosphere-ocean model. A short square pulse, with a duration of nanoseconds, is assumed to be incident at the top of the atmosphere. The polarized signals varying with time and directions are presented for the locations just above and below the atmosphere-water interface and at the bottom of the ocean, and effects of the incidence and disappearance of the external pulse on the Stokes vector components are analyzed. Results in this paper present the general distribution of square-pulse induced polarized signals and they are important for signal analysis in the field of remote sensing using nanosecond pulses.