ABSTRACT Karst regions, where extensive fracture networks accelerate water and nitrogen losses, face severe challenges to ecological restoration, yet how fracture‐filling particle size regulates coupled water–nitrogen dynamics through nonlinear threshold behaviour remains poorly understood. Here, we conducted field soil column experiments under natural rainfall using three fracture‐filling particle size gradations (C0: 3–5 mm; C1: 6–13 mm; C2: 10–30 mm), coupled with PRA and RSS threshold identification. Medium‐sized fractures (C1) achieved the most favourable water retention through a hydraulic conductivity–capillary retention balance: although surface runoff increased relative to C0, the combined runoff and deep leakage loss was lowest in C1 (14.49 mm) versus C0 (16.45 mm) and C2 (16.43 mm). Runoff initiation thresholds consistently ranked C0 > C1 > C2 under both precipitation (124.68, 113.60, 103.27 mm) and antecedent soil moisture (14.79, 10.71, 8.70 mm), with precipitation as the stronger predictor, indicating that coarser fillings lower the activation threshold for preferential flow by enhancing network connectivity. A nitrogen transformation paradox emerged in C1: despite the highest leachate nitrate concentrations (18.34 μg mL −1 ), total nitrogen leaching was ~30% lower than C0, reflecting coupled nitrification–denitrification within its intermediate pore architecture. Runoff thresholds acted as switches for nitrogen loss: leaching increased stepwise only after threshold exceedance, creating nitrogen export hot moments that alternated with safe operating spaces wherein nitrification proceeded without connected leaching pathways. These findings establish fracture‐filling particle size as a structural control valve governing water–nitrogen dynamics through threshold‐mediated mechanisms, providing a mechanistic foundation for precision water and nitrogen management in karst regions.
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