This paper reports a method for directly determining the effective strength of those acid sites on a molecular sieve catalyst that are actually involved in reactions such as hydrodewaxing. The method is here applied to the conversion of a waxy paraffin over a catalyst containing platinum and a SAPO-11 sieve of high isomerization selectivity, as well as a catalyst containing platinum and a H-ZSM-5 zeolite (SiO2/Al2O3 = 150) of high cracking selectivity. Results are compared against the measured Bronsted acid site strength on these molecular sieves determined from temperature-programmed desorption of ammonia and Fourier transform infrared analysis of adsorbed pyridine. Characterization of acid sites showed both concentration and apparent acid strength for H-ZSM-5 higher than those for SAPO-11, with the latter having a finite but smaller amount of strong acid sites that adsorbed pyridine at 573 and 673 K. Reactions with n-hexadecane gave significantly higher conversion rates on H-ZSM-5, and it is shown that a strongly adsorbing molecule like ammonia can be used in situ to estimate the strength of acid sites involved in hydrocarbon conversion steps. Using the method, the "effective acid site strength" for the SAPO-11 catalyst is determined to be about 30 kJ/mol less than on the H-ZSM-5 catalyst. The reactivity of these catalysts is discussed in light of the acid sites and other factors, including crystal structure and size.