Kettle holes are glacially created ponds that form within landscape depressions and are numerous across young moraine landscapes. Kettle hole water budgets are based primarily on winter precipitation, and therefore, undergo pronounced short‐term changes in water level fluctuations. Little is known about kettle hole sediment biogeochemistry in NE Germany, especially with regards to hydroperiod. Our objective for this study was to link the abiotic influences demarked by the evaporative isotopic signal from kettle hole water and solute chemistry to sediment organic matter turnover imprinted in the sediment δ13C and δ15N isotopic values. From the 20 kettle holes we sampled, 19 of these completely dried out, but on different dates. This dynamic was partially explained by longitudinal and elevational changes over the catchment area illustrating regional controls of kettle hole water balance. At the scale of an individual kettle hole, we estimated evaporation explained up to 38% of water volume loss. The changes in water levels were weakly related to differences in surface sediment elemental N and C concentrations between kettle hole edge and centre positions. These dynamics were primarily driven by redox conditions, Ca2+, and several nutrient concentrations (dissolved organic carbon, total dissolved nitrogen, total dissolved P, and ammonium) in the water column. Although we did not detect differences in the surface sediment δ13C and δ15N values, the δ15N signature in relation to the C:N ratio highlights the advanced decomposition state of surface sediment OM in temporarily water filled kettle holes.