The pH within cell wall pores of filter paper fibers and hemp fibers was assessed by Fluorescence Ratio Imaging (FRIM). It was found that the Donnan effect affected the pH measured within the fibers. When the conductivity of the added liquid was low (0. 7 mS), pH values were lower within the cell wall than in the bulk solution. This was not the case at high conductivity (22 mS). The occurrence of the Donnan effect allowed the pH values within pores in normal regions of the cell wall to be compared to the pH in regions with misaligned microfibrils (dislocations) when FRIM was carried out in a low conductivity solution. Surprisingly, no pH difference was observed between normal regions and dislocations, suggesting that pore sizes within the two different regions are approximately the same. In another experiment the Donnan effect was shown to have an effect on hydrolysis of hydrothermally pretreated wheat straw only when conducted in a low conductivity solution and only for xylanase, not cellulases. The hydrolysis experiments indicate that under typical conditions where conductivity is high, the Donnan effect does not lower the pH close to the substrate to an extent that affects enzymatic activity during hydrolysis of lignocellulose.