Current, sea level and bed load transport are investigated in the Great Bay Estuary, New Hampshire, U.S.A. - a well-mixed system with low freshwater flow and having main channel tidal currents over 2 m/sec. Current and sea level forced by the M-2-M-4-M-6 tide at the estuary mouth are simulated by a vertically averaged, nonlinear, time-stepping, finite-element model. The hydrodynamic model uses a fixed boundary computation domain and accounts for flooding-dewatering over tidal flats by making use of a groundwater component. Inertia terms are neglected in comparison with pressure gradient and bottom friction terms, which is consistent with the observed principal dynamic balance for this system. The accuracy of the hydrodynamic predictions is demonstrated by comparison with 5 tidal elevation stations and 2 cross-sectionally averaged current measurements. Simulated current and bottom stress are then used to model bed load transport in the vicinity of a rapidly growing shoal located in the main channel of the lower system. Consisting of coarse sand and gravel, the shoal must be dredged every 5 - 8 years. Two approaches are taken - an Eulerian parametric method in which nodal bed load flux vectors are calculated at each time step and a Lagrangian particle tracking approach in which a finite number of sediment particles are released and tracked. Both methods yield pathways and accumulations in agreement with the observed shoal formation and the long-term rate of sediment accumulation in the shoal area.