We report on Herschel/PACS observations of absorption lines of OH + , H 2 O + and H 3 O + in NGC 4418 and Arp 220. Excited lines of OH + and H 2 O + with E lower of at least 285 and ∼200 K, respectively, are detected in both sources, indicating radiative pumping and location in the high radiation density environment of the nuclear regions. Abundance ratios OH + /H 2 O + of 1−2.5 are estimated in the nuclei of both sources. The inferred OH + column and abundance relative to H nuclei are (0.5−1) × 10 16 cm −2 and ∼2 × 10 −8 , respectively. Additionally, in Arp 220, an extended low excitation component around the nuclear region is found to have OH + /H 2 O + ∼ 5−10. H 3 O + is detected in both sources with N(H 3 O + ) ∼ (0.5−2) × 10 16 cm −2 , and in Arp 220 the pure inversion, metastable lines indicate a high rotational temperature of ∼500 K, indicative of formation pumping and/or hot gas. Simple chemical models favor an ionization sequence dominated by H + → O + → OH + → H 2 O + → H 3 O + , and we also argue that the H + production is most likely dominated by X-ray/cosmic ray ionization. The full set of observations and models leads us to propose that the molecular ions arise in a relatively low density ( 10 4 cm −3 ) interclump medium, in which case the ionization rate per H nucleus (including secondary ionizations) is ζ > 10 −13 s −1 , a lower limit that is several × 10 2 times the highest current rate estimates for Galactic regions. In Arp 220, our lower limit for ζ is compatible with estimates for the cosmic ray energy density inferred previously from the supernova rate and synchrotron radio emission, and also with the expected ionization rate produced by X-rays. In NGC 4418, we argue that X-ray ionization due to an active galactic nucleus is responsible for the molecular ion production.