The Jurassic Lower Carbonate Group in the Aïn Ouarka area of Western Saharan Atlas, Algeria, is represented by six formations, from base to top: Hettangian Chemarikh Dolostone, Early Sinemurian–Pliensbachian Aïn Ouarka Limestone, Toarcian Aïn Rhezala Limestone, Aalenian–Late Bajocian Raknet El Kahla Limestone Breccia, Late Bajocian Theniet El Klakh, and Late Bajocian–Bathonian Tifkirt Limestone formations. From the microfacies analysis, six microfacies types (MF1–MF6) have been recognized and grouped into three associations developed during a transgressive–regressive cycle: (a) inner ramp facies association; (b) middle ramp facies association; and (c) outer ramp facies association. The mineralogical analysis of the carbonate rocks reveals that they contain mostly low‐Mg calcite associated with ankerite, pyrite, and other detrital minerals such as quartz, chlorite, illite, feldspar (albite), and a few clay minerals. These minerals could be related to the deep fluid and hydrocarbon circulations during deposition. The isotopic data display a variation of δ13C isotopic values between −5.14‰ and +2.21‰ (VPDB) and between −8.12‰ and −4.95‰ for δ18O values (VPDB). The set of δ13C values is similar to the signature of marine dissolved inorganic carbon. First of all, the positive values of δ13C show that the origin of carbon is not from the organic‐rich zone (microbial zone), but probably derived from pore‐water and/or biogenic carbonate precursors. On the other hand, the negative values of δ13C indicate that the carbon may result from organic sources linked to the sulphate reduction bacteria activity, or by a heightened volcanic and/or hydrothermal activities releasing light carbon (12C). The negative δ18O values are not consistent with marine water ambient temperature, but with a possible influence of diagenesis or increasing of temperature by hydrothermal water. This hydrothermal activity is controlled by synsedimentary faults during the Early Jurassic and related to a late pulse of the Central Atlantic Magmatic Province (CAMP) volcanism and by regional volcanism during the Middle Jurassic (Bajocian–Bathonian).