A modular electrocoagulation unit, supported by Ca(OH)2 addition to treated water, was operated in the vicinity of a Natura 2000 site for the removal of Cr6+ or Ni2+ from contaminated groundwater. The process was performed at a constant flow rate of 350 L/h. Day 0 concentrations of Cr6+ and Ni2+ started at 91.6 mg/L for Ni2+ and 43 mg/L for Cr and during testing, were decreased by 15%–25%. Residual concentrations of Crtot. and Ni2+ below the required limits of 0.5 mg/L for Crtot. and 0.8 mg/L for Ni2+ can be achieved with the electrocoagulation unit and total removal efficiencies often exceeded 98%. The overall economic assessment showed its feasible application for removal of Cr6+ and Ni2+ on sites with requirements of high environmental protection standards. The polluted area was about 150 × 150 m (22,500 m2), and it contained approximately 78,750 m3 of water contaminated with Cr6+ and Ni2+ (over 41 and 91 mg/L, respectively). The modular arrangement might allow a scaling up. The process’ output could be thus increased according to the number of EC modules in operation.