Micro‐organisms producing microbially induced sedimentary structures, particularly epibenthic cyanobacteria, are not facies‐dependent and could flourish in any environment if appropriate ecological conditions were provided. Hence, the changes in environmental parameters are the controlling factors on ecological tolerance of the producers. This study on the lower Cambrian successions of the Lalun Formation in Central Iran shows that paralic environments reacted differently to changes in parameters such as river and tide energy, palaeo‐topography, the rate of sediment supply and fluctuations in sea‐level, even though all were characterized by sandy substrates suitable for the development of microbially induced sedimentary structures. Therefore, the abundance and preservation of microbially induced sedimentary structures varied in the different paralic environments. From a sequence stratigraphic viewpoint, this study demonstrates that erosional discontinuities lacked the conditions required for the substrate stabilization by microbial communities. The distribution, size and type of microbially induced sedimentary structures within high frequency cycles generally follow the trends of changes in vertical facies stacking patterns. Within systems tracts, the pattern, morphological diversity and size of microbially induced sedimentary structures are not dependent on the type of systems tract, but on the type of depositional system developed such as delta, incised valley, coastal plain, estuaries and shoreline to shelf systems. Generally, estuarine and peritidal carbonates record an increase in the development of mat colonization during the transgressive systems tract, owing to decreased sedimentation rate as well as extended shallow water habitats. In contrast, the existence of microbially induced sedimentary structures depends on the pattern of shoreline shift in depositional systems developed during the highstand systems tract, such as open coast tidal flat and delta environments. If a shoreline regression was continuous (depositional trend and stacking pattern are a set of high frequency cycles), a greater increase in the aggradational component than the progradational component would cause intensified destructive processes hindering the development of microbial communities.