Despite the flotation method allows for the systematic recovery of plant macroremains by processing large amounts of sediment, it is known that water processing can affect plant macroremains leading to their hyper fragmentation or complete destruction as soon as coming into contact with water. In this work a comparison of the results obtained from water processing and hand-picking of wood charcoal remains at the Neolithic site of Tell Qarassa North (south Syria) is presented. The material comes from a burnt roof structure, where a total of 50 hand-picked wood samples and four flotation samples (120.5 l) were recovered. The aim of the work is to evaluate if water processing affects similarly all of taxa or instead, differences exists in the preservation of certain types of remains. To evaluate this, taxonomic and taphonomic analyses were carried out, including the recording of alterations such as vitrification and those related to decay. The results showed large differences in the taxonomic and taphonomic composition of wood remains retrieved in situ and through flotation. While Amygdalus had same proportions in both assemblages, in those derived by flotation, there were greater proportions of Pistacia and lower proportions of Salicaceae. Interestingly, taphonomic analyses showed that the presence of vitrification in samples processed through flotation was twice as high as those handpicked and affected only Pistacia and Amygdalus remains. We need to bear in mind that vitrification is the fusion of different anatomic elements of the wood, which binds the cells and may increase resistance to mechanical damage during processes as flotation. This may explain why vitrification was better represented in the roof samples processed by flotation, since water might have destroyed weaker wood charcoal remains as those not vitrified (i.e. Salicaceae) and therefore, the proportion of vitrified wood charcoal samples would be larger than originally. These results suggest that recovery methods may be introducing biases, particularly in assemblages where features such as vitrification are unevenly distributed among the taxa present at the site. The results presented here warn against straightforward interpretations of wood charcoal frequencies in terms of original composition of past vegetation, and suggest that it would be advisable to use more than one recovery technique, along with recording of different types of alterations, in controlling for over or under-representation of certain taxa.