In our earlier work, silica-based diatom frustules were successfully converted to 3-dimesional F-doped titania-based replicas via shape-preserving gas/solid displacement reactions, and experiments showed that the hydrolysis of organophosphorous ester pesticides, methyl paraoxon (MOX) and methyl parathion (MTH) was significantly faster in the presence of these 3-D titania nanostructures than in the presence of other commercial titania nanoparticles. The enhancement effect of titania frustules appeared to be strongly related to the amount of F-doping on these materials. In this work, a wider range of titania frustule replicas with various F-doping were prepared and characterized, and compared in the hydrolysis of MOX and MTH as well as three carboxylic acids (methyl salicylate, methyl benzoate and methyl 4-(aminomethyl)benzoate). A strong relationship between the amount of F-doping and the enhancement effect on the hydrolysis of organophosphorous esters was still observed. However, such enhancement effect did not occur in the hydrolysis of the carboxylic acids. It was discovered that fluorine-leaching from the titania frustules was significant and yielded high concentration of fluoride ions in the reaction solutions. Dissolved fluoride ions alone could significantly catalyze the hydrolysis of organophosphorous esters but not that of carboxylic acids in the oxide-free systems. It is believed that fluoride ions act as nucleophilic catalysts to accelerate the hydrolysis of organophosphorous esters. Comparison in the hydrolysis product formation from the two potential hydrolysis pathways (i.e., the P-O bond and the C-O bond cleavages) in the studied systems also supports the direct involvement of dissolved fluoride ions in the observed catalytic effect.