The data contains numerical model simulations designed to assess the influence of a) a permeable bed on flow structures above and within the pore spaces of a bed and b) a biofilm streamer on the free flow structure. For the former the data relates to a novel Computational Fluid Dynamics (CFD) model that is able to simulate flow both in the boundary layer flow and Brinkman layer. This allows simultaneous predictions of surface and subsurface flow in one numerical scheme. The analysis is applied to undertake a numerical sensitivity experiment to assess how bed permeability influences flow over bed forms typically found in river channels e.g. dunes. For the latter the data simulates flow around biofilm-streamers in the laminar flow regime. Numerical simulations simulate the flapping motion of a single biofilm streamer. The major thrust of the study is to investigate the impact of changing Reynolds number on hydrodynamic characteristics of the ambient flow and the frequency of biofilm oscillation. Full details about this nonGeographicDataset can be found at https://doi.org/10.5285/a1fbdde5-688d-4b48-9293-12ecf5563704