Natural organic matter (NOM) is a growing concern for artificial recharge plants. In the future, it is predicted that warmer climates and more precipitation will cause higher NOM production in lakes and more NOM transport to lakes. This, coupled with increasing drinking water demand due to the population increase, is pushing operators of water treatment plants (WTPs) to find new ways to treat water. In this study, the possibility of reducing the organic load in infiltration basins through a compact pre-treatment technique utilizing microsieves, or disc filters, instead of bulky sedimentation basins and rapid sand filters after chemical flocculation to separate flocs, was investigated. The experiments were conducted using a laboratory-scale flocculator, bench-scale disc filters (10 µm and 40 µm), FeCl3, an anionic synthetic polymer, and water from Lake Vomb, a lake in southern Sweden. Raw water was flocculated using FeCl3 and the polymer, and the filtrated samples were analyzed by measuring UV–VIS absorbance, total organic carbon (TOC), and permeate volume. The results when using 10-µm and 40-µm disc filters demonstrate that it is possible to reduce NOM (by approximately 50%) and separate flocs from raw water. The experiments also highlight the importance of sufficient flocculation times and the use of appropriate polymer dosage to achieve higher permeate volumes and avoid residual polymers in the effluent. In this paper, the possibility of using this technique as a standalone treatment step or as a pre-treatment step in order to manage the aquifer recharge is demonstrated.