Water prehydrolysis can be used as a pretreatment to extract hemicelluloses and lignin from biomass prior to its conversion into value-added products. In this study, the effects of operational conditions such as reactor system, flow, particle size, and solids content during prehydrolysis of birch wood are compared, using the wood yield as indicator of pretreatment intensity. The results show that both batch and flow-through (FT) systems are equally effective in removing the carbohydrates from the wood. Increasing flow and decreasing particle size and solids content, however, facilitate the removal of lignin. This increased delignification is partly related to a lower extent of condensation reactions. A FT system is also advantageous for the recovery of the extracted sugars because degradation reactions are minimized. Furthermore, by applying elevated temperatures and short retention times, the sugars concentration in the hydrolysate might be only somewhat higher than that in a batch system.