Abstract Nitrate and microbial contamination of groundwater can occur in countries that face intense urbanization and inadequate sanitation. When groundwater is the main drinking water source, as is often the case in such countries, the need to remove these contaminants becomes acute. The combination of two technologies is proposed here, a biological step to denitrify and an electrochemical step to disinfect the groundwater, thereby aiming to reduce the chemical input and the footprint of groundwater treatment. As such, a pyrite-based fluidized bed reactor (P-FBR) was constructed to autotrophically denitrify polluted groundwater. The P-FBR effluent was disinfected in an electrochemical cell with electrogenerated Cl 2 . Nitrate was removed with 79% efficiency from an initial 178 mg NO 3 − L −1 at an average denitrification rate of 171 mg NO 3 − L −1 d −1 , with 18 h hydraulic retention time (HRT). The electrochemical unit achieved a 3.8-log reduction in total coliforms with a 41.7 A h m −3 charge density.