To understand, at a molecular scale, the effect of water on the structure of the amorphous region of polyamide 6,6 (PA6,6), atomistic molecular dynamics simulations have been carried out. Our results concerning the very local water organization relative to PA moieties agree qualitatively with a two-step sorption model. The first sorption mode seems to be saturated well below the lowest water concentration studied (5% relative to the amorphous phase). Moreover, above this saturation, the overall water organization displays at 300 K larger clusters than the 2-3 molecules usually assumed in the literature. The temperature dependence of free volume, hole size, and hydrogen bonding has also been investigated. It shows a transition between plasticized and antiplasticized behavior.