Neural interfaces with increasing channel counts require a scalable means of testing. We present a 512-channel, 4-potentiostat automated multiplexed system for high-throughput electrochemical characterization of neural interfaces. This paper discusses the design philosophy and architecture of the system before demonstrating functionality with electrochemical impedance spectroscopy data, cyclic voltammetry curves, and an example of electrochemical surface modification, all on functional implantable microelectrode arrays currently being used for in vivo electrophysiological studies. Finally, we discuss the limitations to some sensitive or high-frequency impedance measurements due to reactive parasitics.