Capacitive desalination (CDI) is a promising technology for reducing the salinity of brackish water streams. CDI typically employs a nanoporous carbon supercapacitor architecture with the added ability to flow electrolyte through the cell for deionization. Unlike supercapacitors, though, CDI operates with low ionic-strength liquids (e.g., 20 mM NaCl). Characterization in these electrolytes unveils important features in the CV and EIS data that are not commonly observed in supercapacitor studies. Examples of such features are the emergence of a strong “charge-transfer” resistance at mid-to-high frequencies in the EIS spectrum, local minima in the CV curves that are related to a point of zero charge, and potential artifacts due to ion depletion. These features ultimately underlie the system capacitance, device resistance, and effective operational voltage window, which are all strongly related to desalination performance. Here we examine these features in flow-through electrode CDI devices (fteCDI) with activated hierarchical carbon aerogel monoliths (HCAMs) derived from carbonized and activated resorcinol-formaldehyde aerogel. Work at LLNL was performed under the auspices of the US DOE by LLNL under Contract DE-AC52-07NA27344.