The acceleration of urbanization has disrupted natural water cycles, resulting in increased impervious urban surfaces and non-point source pollution from stormwater runoff. Addressing urban stormwater recharge has become crucial. This study introduces a novel silica sand-based permeable filtration material, investigating its surface characteristics, pore structure, permeability, and pollutant interception capabilities. The results demonstrate that hydrophilic binder coating modification of the permeable surface sand aggregate, combined with hydrophilic inorganic additives, having a porous structure with an average pore size of less than 50 μm and a porosity between 15% and 35%, significantly enhances surface hydrophilicity, achieving a permeation rate of up to 6.8 mL/(min·cm²). Moreover, it shows exceptional filtration and anti-clogging properties, achieving over 98% suspended solids interception and strong resistance to fouling. Dynamic biofilm formation experiments using simulated rain and domestic wastewater explore biofilm morphology and function on silica sand filtration well surfaces. Mature biofilms sustain COD removal efficiency exceeding 70%, with levels consistently below 50 mg/L, NH4+ decreasing to 2 mg N/L, and total nitrogen maintained below 10 mg N/L. The system features anoxic, anoxic, and aerobic zones, fostering synergistic organic matter and nitrogen removal by diverse microorganisms, enhancing pollutant mitigation. Silica sand-based permeable filtration material effectively mitigates urban stormwater runoff pollutants—suspended solids, organic matter, and nitrogen—offering an innovative solution for sponge city development and rainwater resource management.