Biofouling in membrane distillation (MD) has several repercussions, including reduced efficiency of the MD process and limiting membrane life. Additionally, the evaluation of MD biofouling using treated effluents from wastewater treatment plants remains an unexplored area. Thus, biofouling formation and development in a long term MD process (15 days) using treated effluent from a wastewater treatment plant was explored in this study. The results revealed that flux decline occurred in four phases: i) initial decline (0–1 d), ii) gradual decline (1–5 d), iii) progressive decline (5–10 d), and iv) rapid decline (10–15 d). Liquid Chromatography-Organic Carbon Detection (LC-OCD) analysis demonstrated that the treated effluent contained humic-like substances, which deposited on the membrane surface in phase 1. Whereas biopolymers development on the membrane surface in phase 2 and 3 was linked to biofouling. Microbial community analysis revealed that the initial colonisers were predominantly thermophilic bacteria, which were different from the microbial community of the treated effluent. The biofilm-forming bacteria included Schlegelella, Meiothermus, and Vulcaniibacterium. These microorganisms proliferate and release excessive extracellular polymeric substances (EPS), leading to the development of mature biofilm on membrane surface. This helped in the deposition of organics and inorganics from the bulk feed, which led to microbial community succession in phase 4 with the emergence of the Kallotenue genus. The results suggested that organic substances and microbial communities on membrane surface at different stages in a long-term MD process had a significant influence on MD performance for high-quality wastewater reuse.