Abstract: A complete hydrogeological understanding of the deep Upper Jurassic carbonate aquifer in the South German Molasse Basin is essential for the future development of this important drinking water resource and geothermally used system. Water chemistry data, δ13CDIC, 14C of the dissolved inorganic carbon (14CDIC) and stable water isotope (δ18O and δD) measurements have been used to evaluate a promising groundwater dating approach with 14C of dissolved organic carbon (14CDOC). The pre-concentration of dissolved organic matter (DOM) was performed by the easy applicable solid phase extraction (SPE) with a styrene-divinylbenzene copolymer sorbent (PPL). Based on the sampling campaign of seven groundwater wells conducted between 2017 and 2019, it was shown that the groundwater is mainly of Ca–HCO3 type with some evidence of ion exchange between Ca2+ and Na+ at two of the investigated wells. The δD values ranged from −89.4‰ to −70.9‰ while δ18O values varied between −12.5‰ and −9.8‰. The obtained stable water isotope signatures indicated that the groundwater is of meteoric origin and was recharged during warm climate (Holocene), intermediate climate and cold climate (Pleistocene) infiltration conditions. The measured 14CDOC activities varied from 5.7 pmC to 51.1 pmC and the calculated piston-flow water ages (ORAs) ranged from 4200 years to 25,248 years using an initial 14C0DOC of 85 pmC. The calculated ORAs showed a very good correlation to the infiltration temperature-sensitive δ18O values which were affirmed with noble gas infiltration temperatures for two wells after Weise et al. (1991) and were also in good accordance with the atmospheric temperature record of the northern hemisphere from Dokken et al. (2015). The results reflect a consistent hydrogeological picture of the carbonate aquifer, which also supports the applicability of the SPE-PPL method for 14CDOC dating in groundwater with a low DOC content (<1 mg/l). In contrast, 14CDIC activities of 1.4 pmC to 21.3 pmC led to geochemically corrected piston-flow ages between 8057 years and >30,000 years and generally to an overestimation of the apparent water ages. This study gives insights into the promising approach of 14CDOC groundwater dating in carbonate aquifers with low DOC contents and allows future sustainable groundwater resource management of the investigated aquifer system.