Despite significant attention directed toward affinity hydrogels as promising platforms for the controlled storage of therapeutic molecular cargo, the loading process remains incompletely understood. Notably, the direct link between surface-level binding interactions and bulk cargo uptake into these hydrogels remains unresolved. Here, we propose a coupling framework for the interplay between microscopic polymer-cargo interfacial interactions and macroscopic bulk uptake dynamics. In contrast to conventional empirical models, our approach explicitly integrates cargo-polymer interaction, enabling the identification of performance limits. Kinetically, we resolve the characteristic loading time as the system transitions between bulk-dominated and hydrogel-dominated kinetic regimes as a function of polymer-cargo binding affinity. Thermodynamically, we demonstrate that cargo permeability within the hydrogel is governed by the product of equilibrium partitioning and diffusivity, thereby revealing water-mediated modulation of cargo uptake efficacy. Collectively, by bridging microscale interactions with macroscale system behavior governing molecular cargo loading in affinity hydrogels, we re-highlight their potential as promising therapeutic storage as well as delivery platforms.