Sapwood thermal properties and water content (Fw) natural variations affect the accuracy of heat pulse sap flow methods, as they are typically set as constants or calculated during zero flow conditions. In a first experiment, a characterisation of both thermal properties and some of their determining anatomical and functional factors was conducted on several fruit tree species assessing the reliability of different methodologies. Besides that, a second experiment was carried out to evaluate the errors of heat pulse methods arising from ignoring Fw variations. To do so, desorption curves were constructed, allowing the substitution of Fw changes with those of water potential (Ψ). Results of the first experiment showed considerable differences between species in both the thermal, anatomical and functional properties of sapwood. Apart from that, discrepancies between the methods applied to determine thermal properties were also found and their implications for some heat pulse methods are discussed. The analysis conducted for the second experiment indicated that large errors in sap flux density (J) determinations might occur when daily and seasonal variations of Ψ (and hence of Fw) are disregarded. The extent of these errors was influenced by the species and heat pulse technique. Thus, the Heat Ratio and Tmax were, respectively, the least and most vulnerable methods to errors in J determinations associated with changes in Fw.