Aims. We probe the physical conditions in the core of Arp 299A and try to put constraints to the nature of its nuclear power source. Methods. We used Herschel Space Observatory far-infrared and submillimeter observations of H2O and OH rotational lines in Arp 299A to create a multi-component model of the galaxy. In doing this, we employed a spherically symmetric radiative transfer code. Results. Nine H2O lines in absorption and eight in emission as well as four OH doublets in absorption and one in emission, are detected in Arp 299A. No lines of the 18O isotopologues, which have been seen in compact obscured nuclei of other galaxies, are detected. The absorption in the ground state OH doublet at 119 {mu}m is found redshifted by ~175 km/s compared to other OH and H2O lines, suggesting a low excitation inflow. We find that at least two components are required in order to account for the excited molecular line spectrum. The inner component has a radius of 20-25 pc, a very high infrared surface brightness (> 3e13 Lsun/kpc^2), warm dust (Td > 90 K), and a large H2 column density (NH2 > 1e24 cm^-2). The outer component is larger (50-100 pc) with slightly cooler dust (70-90 K). In addition, a much more extended inflowing component is required to also account for the OH doublet at 119 {mu}m. Conclusions. The Compton-thick nature of the core makes it difficult to determine the nature of the buried power source, but the high surface brightness indicates that it is either an active galactic nucleus and/or a dense nuclear starburst. The high OH/H2O ratio in the nucleus indicates that ion-neutral chemistry induced by X-rays or cosmic-rays is important. Finally we find a lower limit to the 16O/18O ratio of 400 in the nuclear region, possibly indicating that the nuclear starburst is in an early evolutionary stage, or that it is fed through a molecular inflow of, at most, solar metallicity.
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