Ammonia recovery from wastewater supports sustainable nitrogen circularity and reduces reliance on energy-intensive Haber-Bosch synthesis. Anaerobic digestion effluent represents a concentrated nitrogen resource, yet membrane contactors for selective NH₃ recovery suffer from coupled wetting and fouling in complex real matrices, limiting long-term performance. Conventional hydrophobic modifications improve initial resistance but lack quantitative mechanistic understanding of how interface design governs pore-scale dynamics and sustained transport under realistic conditions. Here we show that systematic fluorosilane engineering of commercial PVDF membranes produces superhydrophobic contactors that, when guided by operando optical coherence tomography, establish a quantitative framework linking interfacial fluorination density to the stabilization of Cassie-Baxter-like states, suppression of pore wetting and fouling, and durable high-efficiency NH₃ recovery from real anaerobic digestion effluent. The optimal PVDF@PFDTMS membrane achieves 98.4% recovery efficiency and 44.8 g m⁻² d⁻¹ flux while maintaining near-invariant porosity and thickness over 20 h and across multiple physical cleaning cycles. These results demonstrate that operando structural diagnostics can transform empirical surface modification into a rational, mechanism-informed design strategy for resilient membrane contactors. This framework advances durable, energy-efficient nutrient recovery technologies for high-strength waste streams and supports scalable nitrogen circularity.