In this paper, a half cycle running mode was adopted to investigate the fouling characteristics of ion-doped polypyrrole/carbon nanotube (PPy/CNT) composite electrodes in capacitive deionization (CDI). The CaCl2 and FeCl3 are used as the typical inorganic model foulants, while the sodium humate is applied as the organic model foulant during the desalting experiments of the CDI with NaCl solution as the basic feed supply. The results indicated that the introduction of Ca2+ or Fe3+ in the supply solution reduces the desalting performance of the CDI, because the solution can be alkalized during the regeneration process of desalting process. In addition, the influence of Fe3+ was greater than that of Ca2+. Concerning the organic fouling of the electrodes, it was found that the incorporation of the sodium humate significantly decreases the desalting performance of the CDI cell, since a higher sodium humate concentration may destroy the structure of the electrode layer and thus the stability of the electrodes.