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. − doublet at 119 µm is found redshifted by ∼175 km s −1 compared with other OH and H 2 O 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 ( 3 × 10 13 L ⊙ kpc −2 ), warm dust (T d > 90 K), and a large H 2 column density (N H 2 > 10 24 cm −2 ). The modeling also indicates high nuclear H 2 O (1 − 5 × 10 −6 ) and OH (0.5 − 5 × 10 −5 ) abundances relative to H nuclei. The outer component is larger (50 − 100 pc) with slightly cooler dust (70 − 90 K) and molecular abundances that are about one order of magnitude lower. In addition to the two components that account for the excited OH and H 2 O lines, we require a much more extended inflowing component to account for the OH 2 Π 3/2 − 2 Π 3/2 5 2− doublet at 119 µm. 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. Our results are consistent with a composite source. The high OH/H 2 O 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 16 O/ 18 O 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.