Recent scanning tunneling microscopy (STM) experiments have shown that, by dosing liquid water to the bare hexagonal boron nitride (h-BN) nanomesh on Rh(111), water dusters can be observed in the nanomesh pores. With the present work, we intend to better understand the nature of the interaction of water with the nanomesh and give indications on the type of structures that have been observed. To this purpose, the corrugated h-BN monolayer on a 12 x 12 Rh(111) slab is calculated, and its structural and electronic properties are studied in some detail. Then the interaction of small water dusters adsorbed on h-BN, with and without the metal, is investigated. The simulation gives insight into the nature of the binding of h-BN to the metal, the role of the corrugation in trapping molecules, and the structure and distribution of the hydrogen bonds formed by the water molecules. Through simulated STM topography, the optimized structures are compared to the experimental results and the most probable configurations of water aggregates within the pore are identified. The results of our calculations suggest that the water aggregates producing the predominant STM images with three protrusions forming an almost equilateral triangle, with side length of about 0.46 nm, are most likely water hexamers.