A persistent gyre at the mouth of the Bay of Fundy results from a combination of tidal rectification and buoyancy forcing (Aretxabaleta et al., J. Geophys. Res., vol. 113, 2008). Here we assess interannual variability in the strength of the gyre using data assimilative model simulations. Realistic hindcast representations of the Gyre are considered over the course of cruise surveys in 2005, 2006 and 2007. Assimilation of shipboard and moored ADCP velocities are used to improve the skill of the simulations, as quantified by comparison with non-assimilated drifter trajectories. Our hindcast suggest a weakening of the Gyre system during May 2005. Retention of simulated passive particles in the Gyre during that period was highly reduced. A recovery of the dense water pool in the deep part of the basin by June 2006 resulted in a return to particle retention characteristics similar to climatology. Retention estimates reached a maximum during May 2007 (sub-surface) and June-July 2007 (near-surface). Interannual variability in the strength of the gyre was primarily modulated by the stratification of the dense water pool inside the Grand Manan Basin. These changes in stratification may be attributed to mixing conditions the preceding fall/winter and/or advectively-driven modification of water mass properties.