The main objectives of the present study are to determine the time-dependent character of bedform dimensions and to assess the feasibility and reliability of dune-tracking techniques to estimate bedload transport in estuarine–marine conditions. A third additional aim is to evaluate the application of the Ribberink bedload transport formula for field conditions with a rippled bed. Field experiments were carried out on Spratt Sand, an intertidal shoal in the mouth of the Teign estuary, Devon, UK. In the framework of the COAST3D project, data of hydrodynamics, bedform development and sediment transport were collected over a period of a month. The presence of sediment on Spratt Sand turns out to be an important factor in the development of bedforms. As soon as sufficient sediment is available—a layer with a thickness of at least 0.20–0.30 m—ripples start to grow and develop into dunes. In general, an increase in bedform height is anticipated to result in an increase in bedload transport. However, the present study demonstrates that the development of dunes instead of ripples may lead to a reduction in migration rates, which, at the end, in reality causes a reduction in bedload transport. The presence of waves appears to be a critical factor to the applicability of the dune tracking technique. Dunes only start to migrate when wave orbital velocities exceed 0.3 m/s. Bedload transport by migrating dunes is generally in the order of 0–1.5 m 2 /s when orbital velocities remain below 0.7 m/s. Bedload transport increases by a factor 2 when wave orbital velocities reach values of 0.8–0.9 m/s. The increase in bedload transport is partly caused by the additional bed shear in the presence of waves. A second wave-generated mechanism is that stronger wave action reduces the effect of hiding which, under low wave–strong current conditions, suppresses sediment pick-up in the sand–gravel mixture. Application of the Ribberink bedload transport formula for conditions with a rippled bed and in case of unidirectional flows with superimposed oscillatory flows leads to a maximum difference between “measured” (dune-tracking) and computed bedload transport up to a factor 2. For low-energetic conditions, the difference is smaller and generally varies between 10% and 20%; for high-energetic conditions this figure amounts maximum 100%.