The gravity-driven membrane (GDM) systems offer a promising solution for decentralized drinking water supply due to its low maintenance and energy consumption. However, research on the practical application of GDM under variable hydrostatic pressure (variable load) and intermittent operation conditions, particularly in response to high-turbidity water, remains limited. This study investigates the long-term performance and characteristics of the biofouling layer of GDM under ultra-low variable hydrostatic pressure (20–60 mbar) and intermittent operation (8–12 h) conditions in practical decentralized water supply. The results indicate that the membrane flux (1.9–6.0 L∙m−2∙h−1, LMH) remained relatively stable despite variations in gravity-driven pressure (ΔP). Long-term operation of GDM can stably remove turbidity and potential pathogens from raw water. The total protein/polysaccharide ratios of extracellular polymeric substances (EPS) in the biofouling layer were below 0.50, reducing contaminant adhesion on the membrane surface. The 0.2–0.4 μm transparent exopolymer particles (TEP) fraction might be crucial for biofouling layer formation. The key species, belong to Proteobacteria and Patescibacteria, significantly alleviated membrane fouling by degrading polysaccharide and proteins in biofouling layer. Comammox Nitrospira were significantly enriched, contributing to efficient nitrification. GDM with variable load maintained a stable flux of 2.2–5.2 LMH under high-turbidity water conditions (300–1200 NTU), and simple forward flushing combined with sludge discharge can quickly restore ΔP. Overall, the variable load GDM system effectively manages membrane fouling and maintains stable filtration performance through the combined effects of variable load and intermittent operation, ensuring long-term and low-maintenance operation for decentralized water supply.