Microalgae dewatering is a major bottleneck for the industrial deployment of microalgal biorefineries due to its high energy and water requirements. This study investigates the optimization and modeling of an industrial-scale aerated submerged ultrafiltration (UF) system for microalgae pre-concentration under real operating conditions. A submerged hollow-fibre Koch LE8 UF module (348 m², 0.03 µm) was operated directly on Chlorella sp. cultures produced in an 800 m² outdoor photobioreactor. Filtration–backwash cycles were experimentally optimized, identifying an optimal sequence of 8.33 min filtration and 1 min backwash, enabling up to 80% net water removal per cycle while maintaining fouling largely reversible under the tested conditions. Long-term trials (6–7 h) achieved stable concentration factors of 3.6–4.3 with complete biomass retention and sustained permeate flux despite increasing solids concentration. Reuse of permeate for backwashing eliminated freshwater consumption without compromising membrane performance. A dynamic resistance-in-series (RIS) model, incorporating mass balances and an empirically derived concentration-polarisation resistance, accurately reproduced permeate flux and biomass concentration dynamics (R² > 0.83) using a single fitted parameter. The validated model was further applied as a digital twin to simulate operation up to the theoretical concentration factor of 10, quantifying the associated energy and water demands. The system exhibited a low estimated specific energy consumption of 1.25 kWh·kg⁻¹ biomass and a water demand of 0.30 m³·kg⁻¹, demonstrating that aerated submerged UF is a robust, scalable, and energy-efficient solution for industrial microalgae harvesting.