Despite extensive research, the environmental and temporal significance of microbial lamination is still ambiguous because of the complexity of the parameters that control its development. A 13 year monitored record of modern fast‐accreting calcite stromatolites (mean 14 mm year−1) from artificial substrates installed in rapid flow in the River Piedra (north‐east Spain) allows comparison of the sedimentological attributes of successive six‐month depositional packages with the known climatic, hydrophysical and hydrochemical parameters of the depositional system. The stromatolites are formed of dense, porous and macrocrystalline composite laminae. The dense and porous composite laminae, which are composed of two to eight laminae consisting largely of calcified cyanobacteria, are characterized by: (i) dense composite laminae, up to 15 mm thick, mostly with successive dense laminae and minor alternating dense and porous laminae; and (ii) porous composite laminae, up to 12 mm thick, consisting mainly of porous laminae alternating with thinner dense laminae. Most of the dense composite laminae formed during the warm periods (April to September), whereas most of the porous composite laminae developed in the cool periods (October to March). Each dense and porous composite lamina represents up to or slightly longer than six months. The alternation of these two types of composite laminae parallels seasonal changes in temperature. The dense and porous laminae result from shorter (for example, intraseasonal) variations in temperature, insolation and hydrological conditions. The macrocrystalline laminae, with crystals >100 μm long, occur isolated and grouped into composite laminae up to 1·7 mm thick. Their occurrence suggests the absence or poor development of microbial mats over periods of weeks to several months. Thus, stromatolite lamination can record different‐order, periodic and non‐periodic changes in the magnitude of environmental parameters over a single year. These results hold important implications for the temporal and environmental interpretation of lamination in microbial structures.