Managed aquifer recharge (MAR) provides means to remove natural organic matter (NOM) from surface waters. Recent studies have explored the degree of NOM removal in groundwater. In this study, we further elaborate the NOM removal at a lakeside natural bank infiltration site that functions as a surrogate for MAR. Our objective was to quantify the carbon budget in the aquifer based on concentration measurements of dissolved (in)organic carbon, and the molecular changes in NOM using Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). According to the carbon budget, only 25% of the dissolved carbon entering the aquifer was organic, and it predominantly originated from lake water. Of the inorganic majority, on average 40% was produced in the vadose zone above the groundwater table, 31% in the lake bank, 22% in the aquifer as a result of degrading organic matter of lake water, and 7% in the lake. Seasonal concentration variations suggested that the lake bank was the main carbon source in the summer, increasing the carbon concentration of infiltrating lake water, that is, 3.0 mg/L to 7.9 mg/L. FT-ICR MS results showed 4960 to 5330 individual compounds in lake and groundwater. NOM removal in the aquifer was selective: the relative abundance of oxygen-containing species decreased from 75 to 31%, while the relative abundance of sulfur-containing species increased from 15 to 57%. The average molecular weights of both species remained unchanged. The study highlighted the role of lake bank processes and sulfur-containing species in groundwater quality.