Gravity-driven membrane (GDM) filtration is promising for decentralized drinking water treatments. To improve the permeability and permeate quality of GDM process, three GDM systems (in-line coagulation system, pre-coagulation system, and system without coagulation as control) were operated in parallel at 65 mbar for 63 days to evaluate the effects of coagulation on flux development, permeate quality, composition and structure of the biofouling layer. The optimal dose of coagulant (polyaluminium chloride) was determined as 4 mg/L. The stable flux increased by 140% and 210% in the in-line coagulation and pre-coagulation systems compared to that of the control system, respectively. Dissolved organic compounds were removed by 31.9% and 29.4% in the in-line coagulation and pre-coagulation systems, while the control system showed a poor removal efficiency (5%). The effective removal of organics from raw water by coagulation resulted in less substrates available in the biofouling layers, thus affecting the production of extracellular polymeric substances (EPS) by limiting the biological processes. The EPS content in the biofouling layer of pre-coagulation system was the lowest, consistent with the highest flux. And such nutrient-poor biofouling layers modified the microbial community, changing the dominant bacteria from Firmicutes to Actinobacteria, thereby affecting the flux. Loose and heterogeneous biofouling layers with numerous holes and cracks were observed under coagulation conditions, which was conducive to the passage of water. All systems exhibited excellent ammonia removal efficiency (96%), but coagulation extended the start-up time for nitrification from 3 days to 5 days. Overall, these results demonstrate that coagulation can improve the GDM filtration performance, and the pre-coagulation system is globally optimal.