Holocene stromatolites are described from Lake Walyungup, a coastal hyposaline lake in south-western Australia. At summer low water, this groundwater-fed depression comprises two permanent shallow water bodies and an ephemeral southern pool, set within an areally extensive littoral zone of variably cemented carbonate crust. Up to 5 m of organic-rich carbonate mud has been deposited within each of these basins in less than 7000 years. Stromatolites rim the water bodies with individual columns up to 2 m tall. Stromatolite-capped tepee structures in subparallel alignment are widespread in the littoral crust, suggesting a linkage between stromatolite growth and zones of groundwater discharge. Lake Walyungup stromatolites, regardless of external morphology and setting, are coarsely laminated and have aragonitic mesoclot microfabrics. These microfabrics are similar to those from lithified portions of active thrombolitic microbialites from nearby Lake Clifton.

Hydromagnesite is a minor to subdominant phase (up to 47 wt%) of the carbonate mineral assemblage in Lake Walyungup. It occurs mainly in the littoral zone as a diagenetic replacement of precursor aragonite, particularly within the mesoclot fabric of stromatolites, but also in sediments (strandline and dune sand, crusts) derived mainly from erosion of stromatolites. In contrast with nonreplaced and impermeable inorganic aragonitic cements, stromatolite mesoclots are microper- meable. Micropermeability is inferred to facilitate hydromagnesite diagenesis. Dolomite is also present in minor amounts as a pore fill in stromatolites, and as a subdominant to dominant (up to 100 wt%) phase in thin, mudcracked micrite layers within the crust package. The layered dolomite may be precipitated directly from the lake water.

Major element abundance of the lake water is: Na+ > Mg2+ » K+ > Ca2+ for cations, and Cl » SO42− ≈ HCO3 > CO32− for anions. Compared to other nearby coastal lakes, Lake Walyungup has a high pH (> 9·0), and an extremely high molar Mg/Ca ratio of > 90. Groundwater in the area has a Mg/Ca ratio generally less than 1. The unusual Mg/Ca ratio in Lake Walyungup is partially a result of in-lake processes with additional minor contribution of Mg2+ sourced from basal marine sand because no Mg-rich bedrock source has been found in the region.