The optimal operating conditions of a combined dissolved air flotation (DAF)-microfiltration (MF) process to respond to changes in raw water quality were investigated by operating a pilot plant for two years. Without DAF pre-treatment (i.e., MF alone), MF operated stably with a transmembrane pressure (TMP) increase of 0.24 kPa/d when the turbidity of raw water was low and stable (max. 13.4 NTU). However, as the raw water quality deteriorated (max. 76.9 NTU), the rate of TMP increase reached 43.5 kPa/d. When DAF pre-treatment was applied (i.e., the combined DAF-MF process), the MF process operated somewhat stably; however, the rate of TMP increase was relatively high (i.e., 0.64 kPa/d). Residual coagulants and small flocs were not efficiently separated by the DAF process, exacerbating membrane fouling. Based on the particle count analysis of the DAF effluent, the DAF process was optimised based on the coagulant dose and hydraulic loading rate. After optimisation, the rate of TMP increase for the MF process stabilised at 0.17 kPa/d. This study demonstrates that the combined DAF-MF process responded well to substantial changes in raw water quality. In addition, it was suggested that the DAF process must be optimised to avoid excessive membrane fouling.