Ambient amplitude modulation atomic force microscopy (AM AFM) is one of the most broadly used techniques as it is versatile and can provide measurements of single nanostructures routinely. Nevertheless, the technique typically measures an apparent height of nanostructures that does not coincide with the true height. Here, we carry out an exhaustive study of the several possibilities that arise in the presence and in the absence of adsorbed water layers when measuring the height of nanostructures. A method to control whether water layers are perturbed and whether intermittent mechanical contact occurs is provided. We show that the predicted range of apparent heights in the several interaction regimes is as large as the experimental values that are routinely obtained. In one extreme the apparent height might be larger than the true height even when sample deformation occurs. In the other, height reversal might occur even when sample deformation is much smaller than the loss of height. A main mechanism leading to such a broad range of measurements is identified in terms of the presence of water layers and the long range character of the resulting forces. In short, due to these long range effects, the gap in separation in the two amplitude branches, i.e., the attractive and the repulsive regimes, might be an order of magnitude larger in the presence of water than in its absence.