Gypsum scaling commonly occurs over cross-flow RO membrane during seawater desalination. It blocks the pores of the semi-permeable membrane and results in substantial permeate flux decline in a shorter time span. The aim of the present study is to understand the gypsum scaling pattern and permeate flux decline through numerical modelling of nucleation, growth of gypsum crystal, and membrane surface coverage using a moment-based population balance method and CFD (computational fluid dynamics). We have performed numerical simulations of gypsum scaling in a roto-dynamic RO filtration system for different combinations of CaSO4 concentrations and feed pressure while NaCl concentration remains the same to match seawater salinity. We have found that the scaling starts where shear rate over membrane is the least and the growth of membrane surface blockage by scaling is controlled by feed pressure and CaSO4 concentration. For higher feed pressure permeate discharge initially is more but stronger concentration polarization causes more scaling and faster permeate discharge decline. Hence, for higher CaSO4 concentrations moderate feed pressure may be suitable but for lower CaSO4 concentrations higher feed pressure may be advantageous.