Interpreting the physical dynamics of ancient environments requires an understanding of how current-generated sedimentary structures, such as ripples and dunes, are created. Traditional interpretations of these structures are based on experimental flume studies of unconsolidated quartz sand, in which stepwise increases in flow velocity yield a suite of sedimentary structures analogous to those found in the rock record. Yet cyanobacteria, which were excluded from these studies, are pervasive in wet sandy environments and secrete sufficient extracellular polysaccharides to inhibit grain movement and markedly change the conditions under which sedimentary structures form. Here, the results of flume experiments using cyanobacteria-inoculated quartz sand are reported which demonstrate that microbes strongly influence the behaviour of unconsolidated sand. In medium sand, thin (ca 0·1 to 0·5 mm thick) microbial communities growing at the sediment–water interface can nearly double the flow velocity required to produce the traditional sequence of ripple→dune→plane-bed lamination bedforms. In some cases, these thin film-like microbial communities can inhibit the growth of ripples or dunes entirely, and instead bed shear stresses result in flip-over and rip-up structures. Thicker (ca≥1 mm thick) microbial mats mediate terracing of erosional edges; they also, foster transport of multi-grain aggregates and yield a bedform progression consisting of flip-overs→roll-ups→rip-ups of bound sand.