High throughput functional assays are increasingly relied upon to generate early and novel discovery leads for drug development. Ion transport proteins including channels, transporters, and pumps play central roles in cellular bioenergetics, excitability, and a multitude of other biological functions. Facile, robust methods for detecting ion transport activity in both native and heterologous systems is desirable for rapid functional analysis and drug discovery for these difficult but important targets. Here we discuss cell-compatible fluorescent probes, functional assays, and VIPR instrumentation that are used to monitor real-time target activity and screen large chemical libraries for potent and selective modulators. Advances and issues for both exogenously applied and fluorescent protein probes of cellular membrane potential, Ca2+, Cl-, and pH are addressed. High throughput screening (HTS) compatible, rapid kinetic and fluorescence resonance energy transfer (FRET) assays are emphasized, in particular the use of voltage-sensitive FRET probes to assay ion channel activity in single cells and 96/384-well formats.