Nitrate (NO3−)-polluted groundwater treatment by enhanced denitrification is becoming increasingly important due to rising NO3− concentrations and decreasing degradation capacities in aquifers. Besides evaluating the efficacy of substrates added to trigger denitrification, secondary reactions must be closely monitored. Biodenitrification by applied organic carbon (Corg) can lead to considerable changes in redox potential (Eh) and pH, two decisive parameters for trace element mobility. In this study, two geologically and hydrogeochemically different groundwater catchments important for drinking water production were investigated and compared. Sediments were analyzed for trace elements as well as sulfur (S) and carbon (C) contents. Ongoing hydrogeochemical reactions were evaluated with depth-specific isotope characterization, and the potential for trace element mobilization by Corg addition was determined in column experiments. Results for enhanced denitrification showed up to 3.8 times lower reaction rates with respect to comparable studies, probably due to incomplete formation of the necessary denitrifying bacteria. Concentrations of trace elements such as nickel (Ni) must also be considered when evaluating enhanced denitrification, as these can negatively affect microorganisms. Added ethanol led to Ni concentrations dropping from 0.013 mg/L to below the detection limit. Thus, Corg addition may not only induce denitrification, but also lead to the immobilization of previously released trace elements.