Lake Van, the world's largest alkaline lake, hosts some of the largest microbialite towers worldwide, which are considered as modern analogues of ancient stromatolites. This study investigates the links between microbialite evolution, geology, climate and hydrology, and the role of biotic and abiotic processes in microbialite growth and morphology. For these objectives, the northern shelf of Lake Van was surveyed by subbottom seismic profiling and diving, and two 9 m and 15 m high microbialite chimneys were sampled at 25 m water depth. Samples were analysed for stable oxygen and carbon isotopes, X‐ray diffractometry, scanning electron microscopy and U/Th age dating. Lake Van microbialites precipitate wherever focused Ca‐rich groundwater flows to the lake floor to mix with alkaline lake water. Variable columnar, conical and branching morphologies of the microbialites indicate various processes of formation by groundwater channelling within the chimneys. Collectively, our data suggest that the microbialite chimneys have formed within the last millennium, most likely during the warm and humid Medieval Climate Anomaly (ca AD 800–1300), when lake level rose approximately to the present level due to enhanced Inputs of riverine Ca‐rich freshwater and groundwater. Our new scanning electron microscopy observations indicate that the internal structure of the microbialites below the outer cyanobacteria‐covered crust is constructed by calcified filaments, globular aggregates and nanocrystals of algal, cyanobacterial and heterobacterial origins and inorganically precipitated prismatic calcite crystals. These textural features, together with dive observations, clearly demonstrate the important role of inorganic carbonate precipitation at sites of groundwater discharge, followed by cyanobacteria and algal mucilage deposition and microbially meditated calcification in the photic zone in the rapid growth of the microbialite chimneys. Considering the close similarities of some textures with those of ancient stromatolites and meteorites, the results of this study provide new insights into the environmental conditions associated with stromatolite formation and extra‐terrestrial life evolution.