Sediment dynamics in tidal flats, ranging from daily to seasonal timescales, are particularly relevant as they control key ecological and geomorphic processes that ultimately contribute to the long-term evolution of coastal and estuarine landscapes. Yet, insights into bed level changes, including the full range of relevant timescales from intra-tidal to daily and seasonal scales, are currently limited due to a lack of efficient methods to record high-resolution (<1 day) data over the long-term (>1 year). Accordingly, this contribution intends to improve our understanding on spatio-temporal patterns of long-term (>1 year) high-resolution (daily) bed level dynamics in tidal flats in relation to the dominant hydrodynamic driving forces, namely tides and waves. Specifically, this study was conducted along two 200 m long cross-shore transects on an intertidal flat located in the macrotidal (>5 m tidal range) Scheldt estuary, Belgium. Results showed that daily bed level changes at the low tidal flat (i.e. 4.10 m below mean high tide level) were dominated by tidal currents, with a strong fortnightly (or spring-neap) signature, whereas wave activity was of secondary importance. Conversely, bed level changes in the high tidal flat (i.e. 0.65 m below mean high tide level) were almost exclusively dominated by wave activity. Additionally, seasonal deposition–erosion cycles that superimposed on the daily bed level changes were associated with the seasonality of wind wave activity and benthic biology. Analysis of wave and current-induced bed shear stresses at the respective locations confirmed this spatial variability of tidal-dominated sediment dynamics at the low tidal flat versus wave-dominance at the high tidal flat, and comparison with local critical bed shear stresses for sediment motion also revealed differences in morphological impacts of the hydrodynamics between the two transects. These distinctive responses of bed level dynamics across the tidal flat can be partly explained by the spatially varying sediment properties across the tidal flat and may be further mediated, on a seasonal time scale, by the growth of the algal mat with its effect on stabilizing the sediment bed. In view of the large spatial and temporal variability of internal and external forcing revealed in this study, comprehensive and detailed field measurements are even more necessary to understand and predict long-term bed level dynamics and related ecological implications in tidal flats.