A Lagrangian particle method embedded within a 2-D finite element code, is used to Study the transport and ocean-estuary exchange processes in the well-mixed Great Bay Estuarine System in New Hampshire, USA. The 2-D finite element model, driven by residual, semi-diurnal and diurnal tidal constituents, includes the effects of wetting and drying of estuarine mud flats through the use of a porous medium transport module. The particle method includes tidal advection, plus a random walk model in the horizontal that simulates sub-grid scale turbulent transport processes. Our approach involves instantaneous, massive [0(500,000)] particle releases that enable the quantification of ocean-estuary and inter-bayexchanges in a Markovian framework. The effects of the release time, spring-neap cycle, riverine discharge and diffusion strength Oil the intra-estuary and estuary-ocean exchange are also investigated.