Batch incubation and column percolation experiments with dissolved organic matter solution at different pH values were performed to investigate the effect of organic matter sorption and microbial activity on the wettability of clean quartz sand particles. Sodium azide was used as a biocide to control microbial activity. Changes in wettability were evaluated by contact angle measurements. Wettability of the quartz sand was found to significantly decrease after sorption of organic matter. An adsorbed C content of <0.1 g C kg−1 turned out to be effective in increasing the contact angle from initially 30 to >70°. Results of the percolation experiments revealed that the change in contact angle was depth dependent, with the greatest increase in the upper part of the columns. The low C/N ratio (<10) of the organic matter adsorbed in the upper part of the sand columns percolated without biocide addition suggested that the depth dependency was caused not only by sorption of organic matter but also was affected by microbial activity. This finding was supported by an increasing contact angle for sand columns percolated with a solution close to neutral pH (6.7), where more favorable living conditions for bacteria could be assumed. We also observed a trend of a linear inverse relationship between C/N ratio and contact angle, i.e., increasing contact angle with decreasing C/N ratio. Overall, the results indicated that the formation of biogeochemical interfaces can strongly change the original wetting properties of mineral particle surfaces.