This study concentrates on Viséan Strathclyde Group microbial carbonates from the eastern Midland Valley of Scotland. In the largely non-marine Sandy Craig and West Lothian Oil-Shale formations persistent lithostratigraphical marker horizons, such as distinct microbial carbonates, are used to aid correlation of sequences where conventional biostratigraphy is limited to the identification of infrequent marine bands. In the newly described Rosyth core, microbial carbonates above the Burdiehouse Limestone are correlated with microbial horizons at Kingswood (Fife) and Inchkeith (Firth of Forth), a correlation supported by the presence of the bivalve Curvirimula scotica. The revised position of the Inchkeith microbial horizon to 20–30 m above the Burdiehouse Limestone contradicts earlier correlations of the Inchkeith sequences with the Burdiehouse Limestone. The microbial carbonates represent littoral and sublittoral zone stromatolites growing in <20 m of water. The best modern analogues are stromatolites forming in East African Rift Valley lakes. These microbial carbonates formed in volcanically isolated shallow sub-basins or in association with delta progradation. Lavas and tuffs provided stable substrates free of clastic sediment for stromatolite nucleation, and their weathering may have enhanced Ca2+ ion activity to promote carbonate precipitation. These lacustrine microbial carbonates cannot be implicitly linked with climatic events or basin-wide regression as has been proposed for a regionally persistent microbial carbonate below the Burdiehouse Limestone.