I am not an expert in this Sanath but roughly thinking I would suggest the electrochemical cells as this gives the possibility to select your electrodes. Hence according to reduction potential of different materials you'd be able to select the most appropriate one to recover the metals in water.
In my openion, electrochemical systems were most preferable where your target is only metal recovery.
But if you are targeting both wastewater treatment and metal recovery then you can prefer Microbial fuel cells where simultaniously both will occur. Really a nice question. keep it up.