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The Cretaceous was punctuated by episodic flooding of continental margins forming epicontinental seas. The Trans‐Sahara Seaway was one of these epicontinental seas, connecting the Gulf of Guinea with the Tethys Ocean. In this study, data including microplankton abundances, stable carbon isotopes of organic material and elemental geochemistry were integrated with traditional sedimentological analyses from the Trans‐Sahara Seaway. The carbon isotopic data provide the first evidence that oceanic anoxic event 2 was present in the Trans‐Sahara Seaway, and palynology shows it was associated with an increase in peridinioid dinocyst abundance. A combined study of microplankton assemblages and sedimentology reveals palaeoenvironmental trends linked to sea‐level change. Lowstand system tracts were characterised by increased siliciclastic grain size, low microplankton diversity, and were dominated by Chlorophyceae. Transgressive system tracts were associated with diversity increases during rising sea level, with open marine gonyaulacoid dinocysts dominating the assemblages. Maximum flooding surfaces were recognised by the highest increase in biological diversity in argillaceous deposits. As sea level started to fall, the peridinioid dinocysts became dominant, with decreased microplankton diversity during highstand systems tracts. This combination of sedimentology and interpretation of dinocyst assemblages allows the identification of shallow to deeper marine depositional sequences of Cenomanian–Santonian strata within the Yola Sub‐basin. This approach could be used to delineate marine depositional sequences where using conventional sedimentological methods alone is very challenging. [ABSTRACT FROM AUTHOR]