This paper presents an analysis of the fouling of a ceramic membrane by a mixture containing high concentrations of humic acid and colloidal silica during cross-flow ultrafiltration under various operating conditions. Two types of feed water were tested: feed water containing humic acid and feed water containing a mixture of humic acid and colloidal silica. The colloidal silica exacerbated the fouling, yielding lower fluxes (109–394 L m−2 h−1) compared to the humic acid feed water (205–850 L m−2 h−1), while the retentions were higher except for the highest cross-flow rate. For the humic acid feed water, the irreversible resistance prevails under the cross-flow rate of 5 L min−1. During the filtration of an organic–inorganic mixture, the reversible resistance due to the formation of a colloidal cake layer prevails under all operating conditions with an exception. The exception is the filtration of the organic–inorganic mixture of a 50 mg L−1 humic acid concentration which resulted in a lower flux than the one of a 150 mg L−1 humic acid concentration under 150 kPa and a cross-flow rate of 5 L min−1. Here, the irreversible fouling is unexpectedly overcome. This is unusual and occurs due to the low agglomeration at low concentrations of humic acid under a high cross-flow rate. Under lower transmembrane pressure and a moderate cross-flow rate, fouling can be mitigated, and relatively high fluxes are yielded with high retentions even in the presence of nanoparticles. In this way, colloidal silica influences the minimization of membrane fouling by organic humic acid contributing to the control of in-pore organic fouling.