Recovering ammonia from wastewater by membrane distillation (MD) is a sustainable approach to alleviate environmental stress, as well as reduce energy consumption from the Haber−Bosch process. MD utilizes the low-grade heat and leverages the volatility of ammonia for ammonia transport; however, the concurrent transport of water and ammonia molecules and their mutual influence, remains unclear. In this study, we combine experiments and a mathematical modeling approach to investigate both individual and combined water transport and ammonia transport from ammonia-rich wastewater in MD. The water flux exhibits minimal variation in response to changes in feed solution composition and pH value, while the ammonia flux demonstrates significant sensitivity to the pH variation of the feed solution. Although both water transport and ammonia transport increase with the increasing feed solution temperature, our simulation reveals that the water mass transfer coefficient remains unchanged, while the ammonia mass transfer coefficient varies in tandem with temperature changes. We analyze the ammonia-to-water transport selectivity (ρ), noting that a lower temperature yields a higher ammonia-to-water selectivity (ρ = 25.9 at 30 °C to ρ = 6.8 at 60 °C), and the selectivity is more sensitive at lower temperatures. The selectivity decay analysis indicates that the ammonia-to-water mass transfer ratio is a key factor that tunes the selectivity with respect to feed temperature variation. This integrated experimental and simulation study provides valuable insights into ammonia and water transport toward selective ammonia recovery in MD.