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Wave-Powered Reverse Osmosis (WPRO) represents a promising convergence of ocean energy harvesting and advanced Reverse Osmosis (RO) desalination techniques. The significant fluctuations in pressures and flow rates within the integrated WPRO system present a critical challenge, necessitating an accurate transient model for effective performance estimation. This study presents a two-dimensional transient model based on pressure-correction algorithm to simulate channel flow with membrane boundary conditions under varying inlet conditions. The coupled dynamics of pressure, velocity, and salt concentration are addressed iteratively by decoupling and updating each term separately. The model investigates the performance of RO systems under different input conditions, including constant, sinusoidal, and irregular flow. The results indicate that constant input with higher pressure and lower flow rate achieves a better Recovery Ratio (RR). It is emphasized that for WPRO systems, a fair comparison requires choosing the same average power or pressure when evaluating different inputs. Under equivalent input power, sinusoidal waves result in a lower RR compared to constant inputs due to reduced average pressure. Conversely, under equivalent inlet pressure and flow rate, sinusoidal waves achieve a higher RR than constant inputs due to the phase difference between pressuredriven permeate velocity and diffusion-driven Concentration Polarization (CP). Specifically, sinusoidal inputs with higher frequency and higher amplitude display a higher RR. Additionally, irregular input yields a higher RR than constant inputs, as mean pressure and power can be maintained at levels comparable to those of constant input. The model’s adaptability to diverse flow regimes — from steady to sinusoidal and irregular fluctuations — highlights its potential as a critical tool for optimizing RO desalination processes powered by renewable ocean energy.