Lacustrine stromatolites of the Norian Arnstadt Formation (“Steinmergelkeuper”) occur on top of asymmetric flooding–evaporation cycles of a closed lake basin. They have been investigated with regard to associated lithofacies and biota, microfabric and stable carbon and oxygen isotopes. The stromatolites of the “Middle Grey Series” are brecciated and reworked by a flooding event of a subsequent lake cycle. They comprise agglutinated stromatolites rich in fish scales as well as skeletal stromatolites composed of a rhythmically grown dendroid micropeloidal framework. The latter are characterized by a shift towards positive δ13C values relative to the associated lake carbonates. This points to an effective photosynthesis in biofilm calcification at low concentrations in dissolved inorganic carbon (DIC) in a perennial fresh to brackish water lake. The stromatolites of the “Upper Red Series” occur on top of perennial lake cycles intercalated between playa lake deposits. The fine-grained stromatolites are poor in microfabric characteristics but show a significant covariation of δ18O and δ13C. This points to evaporation/degassing acting as driving mechanism in biofilm calcification. The lack of biotic effects on carbon isotope fractionation may reflect high concentrations in dissolved inorganic carbon. Skeletal oncoids, which occur as allochthonous components within an intraformational lag deposit of the “Upper Red Series”, are composed of cyanobacterial tubes and probably represent lowest saline lakes with only poor DIC buffering. Stable isotope signatures in conjunction with stromatolite microfabric analyses may be used as a proxy of DIC concentrations in ancient closed lakes.