Fouling phenomenon is well known as a main obstacle in membrane separation technology. In this study, the effects of bubbling with various hydrodynamic factors and gas–liquid solubility were evaluated on fouling control and permeation flux in ultrafiltration of skimmed milk solution. Direct gas injection and carbonated feed, as a new bubbling method, were used for bubbling. In the direct gas injection technique, various two-phase flow patterns (slug and bubble), gas flow rates, and bubbling modes (continuous and intermittent) were investigated during a cross-flow ultrafiltration. The results showed that the both of gas bubbling methods improved the permeation flux during 30-min filtration. The permeation flux was enhanced up to 72 and 40% by direct injecting of N2 and CO2, respectively, while it was only enhanced up to 58% with carbonated feed. The evaluation of hydrodynamic resistance of membranes indicated that the gas bubbling by carbonated feed was more effective on the fouling resistance, while the cake resistance was affected by the gas injection during infiltration. In addition, the slug flow pattern was more effective than the bubble flow pattern on decline of membrane fouling. In the slug flow pattern, the permeate flux increased when medium flow rate was applied. Furthermore, ultrafiltration performance was improved using the intermittent gas bubbling mode. This study indicated that slug flow pattern with insoluble gas has a higher performance than the other ones in preventing fouling and flux enhancement during ultrafiltration processing.