<p>Reverse osmosis (RO) is increasingly applied for the reclamation of ammonia-rich wastewater. However, the mechanisms governing NH₃/NH₄⁺ transport across RO membranes remain unclear. In this study, we develop an ammonia partitioning and transport (APT) model to quantitatively describe NH₃/NH₄⁺ retention and transport, incorporating pH-dependent NH₃/NH₄⁺ partitioning and membrane charge variation. The theoretical model is validated through laboratory-scale RO experiments under varying pressures, feed concentrations, and pH conditions. In contrast to stable water permeability, the permeability coefficient of total ammonia nitrogen (TAN) is sensitive to pH value. TAN retention is optimal (89.1 ± 3.2%) near neutral pH, decreasing at higher pH due to increased NH₃ fraction and at lower pH due to reduced membrane charge. By decoupling diffusion, advection, and electromigration, the APT model shows distinct NH₄⁺ and NH₃ flux contributions, revealing pH-dependent transport mechanisms governed by speciation and membrane charge. Molecular dynamics simulations further differentiate the transport pathways of NH₃ and NH₄⁺, showing that NH₄⁺ experiences a significantly higher energy barrier. Validations with both synthetic and real manure streams demonstrate good predictive accuracy for advancing RO applications in ammonia-rich streams.</p>