The permeability of fault zones impacts diverse geological processes such as hydrocarbon migration, hydrothermal fluid circulation, and regional groundwater flow, yet how fault zones affect groundwater flow at a regional scale (1-10 km) is highly uncertain. The objective of this work is to determine whether faults affect regional patterns of groundwater flow, by using radioactive radon and chloride to quantify groundwater discharge to lakes underlain by faults and not underlain by faults. We sampled lakes overlying the Paleozoic Appalachian fold and thrust belt in the Eastern Townships in Québec, and compared our results to a previous study in a crystalline watershed in the Canadian Shield. The field data was analyzed with an analytical geochemical mixing model. The uncertainties of model parameters were assessed in a sensitivity analysis using Monte Carlo simulation, and the difference between lakes tested with statistical analysis. While the model results indicate non-negligible groundwater discharge for most of the lakes in the Paleozoic orogen, the difference between the groundwater discharge rate into the lakes located on faults and the other lakes is not statistically significant. However, the groundwater discharge rate to lakes in the Paleozoic orogeny is significantly higher than lakes that overlay crystalline bedrock, which is consistent with independent estimates of permeability. The rate of groundwater discharge is not significantly enhanced or diminished around the thrust fault zones, suggesting that in a regional scale, permeability of fault zones is not significantly different from the bedrock permeability at shallow depth in this old, tectonically-inactive orogen.