Ion beam processes related to focused ion beam (FIB) milling, surface patterning and secondary ion mass spectrometry (SIMS) require precision and control, the quality and cleanliness of the sample being a detrimental factor. Furthermore, several domains of nanotechnology and industry use nano-scaled samples that need to be controlled to an extreme level of precision. To reduce the irradiation-induced damage and to limit the interactions of the ions with the sample, low energy ion beams are used due to their low implantation depths. Yet, low energy ion beams come with a variety of challenges. Indeed, for such low energies, the residual gas molecules in the instrument chamber can adsorb on the sample surface and impact the ion beam processes. In this paper we pursue an investigation on the effects of the most common contaminant, water, sputtered by ultra-low energy ion beams, ranging from 50 to 500 eV and covering the full range of incidence angles, using Molecular Dynamics (MD) simulations with the ReaxFF potential. From this study we show that the expected sputtering yields trends are respected down to the lowest sputtering yields, a region of interest with low damage being obtained for incidence angles around 60 to 75°. We also demonstrate that higher energies induce a larger removal of the water contaminant and at the same time induce an increased amorphization, which produces a trade-off between sample cleanliness and damage.