In soft-bottom marine ecosystems, bedform variation is induced by wind- and tidal-driven hydrodynamics. The resulting megaripples, sand waves and sandbanks form a spatially and temporally heterogeneous seafloor landscape. The strong physical forces imposed by the migration of these bedforms are important determinants for the occurrence of different macrozoobenthic species. Quantifying the effect of these forces can help in differentiating natural- and anthropogenically induced physical stressors. However, large-scale mapping of seabed morphology at high resolution using multibeam echosounder is challenging, costly and time-consuming, especially in shallow seas, prohibiting wide swaths. Instead, their bathymetry is typically studied using single-beam transects that are interpolated to bathymetric grids with a relatively coarse resolution (20 m). However, this leaves out information on smaller scale (<20 m) bedforms that can be ecologically relevant. In the Dutch Wadden sea, a shallow tidal system, we characterized bedform variation at high resolution using single-beam data for the first time. We calculated a 2-D Terrain Ruggedness Index (TRI) at sub-meter resolution along the single-beam transects and interpolated the results to a full 3-D grid. We then validated the result by relating TRI to independently modeled hydrodynamic parameters and to the distribution of macrozoobenthic species. We found that TRI successfully integrates the variation of tidal-driven bed shear stress and wave-driven orbital velocity. In addition, we found TRI to be a good predictor of the occurrence of macrozoobenthic species. The inferred small-scale bedforms provide valuable information for separating the relative importance of natural dynamics versus anthropogenic disturbances such as dredging and bottom trawling activities. We discuss that by repurposing already available single-beam data in this way, bedforms can be characterized at high resolution without the need for additional equipment or mapping campaigns, yielding novel input to decision-making on marine management and conservation.