A system and apparatus for biomethanation and removing carbon dioxide from the methane comprises (a) a primary anaerobic digester adapted and arranged to generate a biogas mixture comprising methane and carbon dioxide from organic materials; (b) an electrochemical reactor adapted and arranged to capture carbon dioxide from the biogas as bicarbonate and to generate hydrogen by electrolytic water slitting, and (c) a biomethanation reactor adapted and arranged to convert the bicarbonate and hydrogen from the electrochemical reactor to methane. The electrochemical reactor also acidifies a saline process stream from the biomethanation reactor and returns the acidified process stream back into the biomethanation reactor for pH control in the biomethanation process.