The filling of nanometer and sub-nanometer channels/tubes with water governs applications ranging from desalination and filtration to nanoscale energy conversion. Here, we report the most nonintuitive entropy-dominated filling of mildly hydrophilic boron nitride nanotubes (BNNTs) with diameters ranging from 0.85 to 1.69 nm. For all the BNNT sizes, water inside the BNNT is more stable than water in the bulk. The factor dictating the favorable nature of the entropy depends on the specific-BNNT-diameter-dictated structure of the water molecules. For example, for the 0.85 nm BNNT, the rotational entropic component dominates due to the presence of a significant fraction of the dangling water OH bonds that do not participate in hydrogen bonding. The fraction of such dangling OH bonds (the average HBs per molecule) decreases (increases) with an increase in the BNNT diameter, leading to a progressively reduced contribution of the rotational entropy. For the 1 nm BNNT, the translational entropic component dominates due to the enhanced in-plane motion of the water molecules caused by the single-file nature of water molecules spanning a significant radial expanse inside the BNNT. For larger BNNTs, translational entropy decreases with an increase in the BNNT diameter, although it remains the dominant factor governing the entropy-driven filling of BNNTs. This favorable translational entropy for larger BNNTs can be associated with (1) the presence of chain-like regions formed by water in 1.13 nm BNNT and (2) the presence of a high specific water volume and reduced number of HBs per molecule (as compared with bulk water) in 1.27, 1.41, 1.55, and 1.69 nm BNNTs.