This study documents the processes involved in forming flaser and wavy bedding governed by microbial activity in sediments. It focuses on a modern marginal‐tidal system providing evidence of the role that biofilms play in the stabilization of ripples and their potential preservation. A combination of detailed field work, analysis of water level records and microscopic petrographic inspection were used to reply to the question: how fine‐grained and coarse‐grained sediments can sequentially be deposited and preserved in a coastal environment. The hydraulic energy was measured by water level sensors recording flooding events that inundate the colonized tidal flat. Changing surface morphologies were monitored after storms, revealing the importance of biological processes in the preservation of ripples. A mud drape over ripples was observed several days after the undulated surface formation, known as a sinoidal sedimentary structure, which is a thin biofilm covering the ripples, caused by the presence of a microbial mat. Because bedforms are essential predictors of palaeoenvironmental reconstruction, interpretation in the geological record should take into consideration the important effect that colonized sediments have on the preservation of ripples. A geobiological model explains the flaser sedimentation, common in depositional coastal environments, suggesting that the hydrodynamic conditions may not be directly reflected by the grain size at the time of deposition. The study reveals that flaser sedimentation involves an interaction with benthic organisms, reflected by the sequence of microbial mats with sand ripple marks. A detailed description of heterolithic sequences shows that the presence of microbial activity can drive ripple preservation. This suggests that hydraulic interpretation of the sedimentary record based only on physical processes might be erroneous.