Profound environmental changes punctuated the Early Jurassic period, as recorded by marked carbon and oxygen isotope anomalies and major biotic crises. The response of low-latitude regions of Northern Gondwana to such intense changes is not documented as well as that of other Tethys areas. We present new calcareous nannofossil assemblages from three sections located in NW Algeria, in the Sahara and Tlemcen Basins, respectively. New stable carbon and nitrogen isotope data are provided from the Tlemcen Basin to reconstruct local environmental conditions in the wider context of a Toarcian greenhouse climate. We first established a solid chemo- and biostratigraphic framework by integrating stable carbon isotope data and calcareous nannofossil events. Calcareous nannofossil assemblages show common trends in the two basins, such as the occurrence in high proportions of the deep-dweller species Mitrolithus jansae, likely indicating stratification of the water column with a deep nutricline. This taxon dominated the assemblage during the negative carbon isotope excursion (CIE) interval, often used to delineate the base of the Toarcian anoxic event (T-OAE). Such a nannofossil record is unique in the Western Tethys domain, as M. jansae is known to drastically decrease in abundance during the T-OAE until its disappearance in the aftermath of the event. The NW Algeria nannofossil record indicates prolonged thermal stratification of water-masses, finally triggering hyper-oligotrophy and low productivity in shallow waters during the Toarcian CIE. Such peculiar conditions are likely related to the combined effects of a warm and arid climate dominating along the northern Gondwana margin and the presence of a strong clockwise gyre over the epicontinental shelf, which brought warm equatorial waters from the Tethys Ocean to the NW Algeria shelf.