This long-term pilot-scale study on the performance of ceramic microfiltration (CMF) was conducted at the Bangkhen water treatment plant (BWTP), with the raw water from Chaophraya River, Thailand. Raw water turbidity and dissolved organic carbon (DOC) were varied in the ranges of 20–210 NTU and 3.0–8.5 mg/L respectively. The hybrid pilot-scale CMF (Pilot-CMF) operational parameters were optimized with the aid of jar-tests and laboratory-scale CMF (Lab-CMF) operations. The systems were operated with various polyaluminum chloride dosages and filtration cycle times. Pilot-CMF provided excellent steady turbidity removal compared to the conventional water treatment process. DOC removal percentages of Pilot-CMF and the conventional process at the BWTP were 49% and 30% respectively. With different coagulant dosages, unique patterns in transmembrane pressure (TMP) variations were observed. The daily TMP increment under low turbidity conditions was 0.08 kPa/day. During rainy periods (turbidity over 100 NTU) the TMP increment reached 0.79 kPa/day. However, once the turbidity of raw water reaches normal conditions (30–60 NTU at the BWTP) the Pilot-CMF system recovers the TMP increment due to efficient backwashing.