In this paper we present the detection of H2O and OH+ emission in z>3 hot dust-obscured galaxies (Hot DOGs). Using ALMA Band-6 observations of two Hot DOGs, we have detected H2O(2_02-1_11) in W0149+2350, and H2O(3_12-3_03) and the multiplet OH+(1_1-0_1) in W0410-0913. We find that both sources have luminous H2O emission with line luminosities of L_H2O > 2.2x10^8 Lsol and L_H2O = 8.7x10^8 Lsol for W0149+2350 and W0410-0913, respectively. The H2O line profiles are similar to those seen for the neighbouring CO(9-8) line, with linewidths of FWHM ~ 800-1000 km/s. However, the H2O emission seems to be more compact than the CO(9-8). OH+ is detected in emission for W0410-0913, with a FWHM=1000km/s and a line luminosity of L_OH+ = 6.92x10^8 Lsol. The ratio of the observed H2O line luminosity over the IR luminosity, for both Hot DOGs, is consistent with previously observed star forming galaxies and AGN. The H2O/CO line ratio of both Hot DOGs and the OH+/H2O line ratio of W0410-0913 are comparable to those of luminous AGN in the literature. The bright H2O(2_02-1_11), and H2O(3_12-3_03) emission lines are likely due to the combined high star formation levels and luminous AGN in these sources. The presence of OH+ in emission, and the agreement of the observed line ratios of the Hot DOGs with luminous AGN in the literature, would suggest that the AGN emission is dominating the radiative output of these galaxies. However, followup multi-transition observations are needed to better constrain the properties of these systems.