To assess the response of northern peatlands to hydrological changes, we analysed the response of a model designed to simulate peatland development at a millennial timescale, the Holocene Peat Model, to two hydrological drivers. The study is performed on two open ombrotrophic peatlands located in the James Bay region in North-eastern Canada. For both sites, two simulations were realized: one based on a precipitation reconstruction from pollen data, used as input in the model, and a second using a water-table depth reconstruction derived from testate amoebae to apply a forcing on the model. Simulated variations in carbon accumulation rates (CARs) and vegetation composition were analysed against palaeoecological datasets. In both sites and for the two hydrological drivers, modelling results in CARs showed periods of net carbon loss that coincided with fluctuations in observed CARs, although net carbon loss cannot be traced in palaeoecological datasets per se. The comparison between plant macrofossil records and simulated vegetation distributions highlighted differences between precipitation and water-table depth-driven simulations. Thus, the methodology used was found useful to analyse the origin of vegetation shifts in macrofossil datasets.