The presence of Fe2+ and Mn2+ would cause severe ultrafiltration (UF) membrane fouling and limited its extensive application in treating the groundwater. A pilot-scale gravity-driven membrane (GDM) process which coupled the dual roles of biocake layer and UF membrane was introduced to treat the groundwater under high Mn2+concentrations and low temperature conditions. The results indicated that flux stabilization was observed during long-term GDM filtration with average stabilized fluxes of 3.6–5.7 L m−2 h−1. GDM process conferred efficient removals of Fe2+ and Mn2+ with both average removals > 95%. Pre-adding manganese oxides (MnOx) could effectively shorten the ripening period of manganese removal from 50 to 30 days, and simultaneously contribute to the Mn2+ removal and flux improvements. The presence of Mn2+ facilitated the formation of heterogeneous structures of biocake layer to primarily determine the flux stabilization of GDM, while the influence of extracellular polymeric substances (EPS) concentrations was nearly negligible. Besides, the Mn2+ removal was primarily attributed to the biocake layer other than UF membrane itself, and the chemically auto-catalytic oxidation by MnOx particles played the pivotal role. Therefore, these findings provide relevance for establishing new strategies in treating the iron-and manganese-containing groundwater.