Managed aquifer recharge (MAR) refers to intentional infiltration of surface water to an aquifer for facilitating natural water treatment and storage. MAR is often used as a treatment to remove natural organic matter from water in drinking water production. The sustainability of MAR depends on how the aquifer capacity to remove organic matter will evolve over the long term. This report explores the behavior of MAR systems by using a natural lake–aquifer system as a surrogate. Natural infiltration of lake water to groundwater has been going on for millennia at the research site in Finland chosen for this study. According to the measurements, the mean concentration of total organic carbon (TOC) in lake water was 3.0 mg/L. Within the distance of 3 m from the lake bank (retention time 7–15 days), already 46% of TOC was removed. At greater distances along the flow paths within the aquifer, 80–90% of TOC was removed. The observed TOC removal in the aquifer was slightly higher than the reported values at MAR sites, indicating that MAR can be an effective solution to the problem of removing natural organic matter in the long term. Signs of accumulation of organic matter were not observed in the aquifer, which suggests that biodegradation was the main removal method, and the role of sorption was minor. Several processes had an impact on oxygen levels in the aquifer, which led to spatial and seasonal changes in the redox conditions and in the iron and manganese concentrations in groundwater.