The protection of the globally widespread lentic small water bodies (LSWB) must be based on detailed knowledge about their hydrological connectivity and water balance. The study aimed to identify and quantify water balance components as well as surface‐groundwater interaction of two LSWB in a characteristic lowland region with a combination of different methods. This includes the collection of hydrological data and the use of bromide and water stable isotopes (δ2H and δ18O) as tracers. With their help, mixing models were established, and daily water balances were assessed. The results show a strong bidirectional interaction of both LSWB systems with shallow groundwater. Bromide and stable isotope tracers allowed for the identification of the most relevant in‐ and outflow sources and pathways. Thereby, isotope data revealed isotopic enrichment typical for open‐water bodies and only minor precipitation inputs mainly relevant at the end of the dry season. Water balance calculations suggested accentuated seasonal dynamics that were strongly influenced by shallow groundwater, which represented large inputs into both LSWB. By that, different phases could be identified, with high inflow rates in winter and spring and decreasing fluxes in summer. In one LSWB, a drainage system was found to have a major impact next to the shallow groundwater interaction. The findings of this research provide detailed insights into the influence and importance of shallow groundwater for LSWB in lowland regions. This impacts the diffuse input of agricultural pollutants into these ecologically important landscape features.