The Middle Miocene rocks in the northern part of the Western Desert of Egypt are dominated by carbonate rocks that constitute the Marmarica Formation. To determine the depositional environments and sequence architecture of the Marmarica Formation, three sections were described and sampled in detail. These sections from west to east are; Girba, Naqb El‐Migahhiz, and Gabal Umm Hiyus. The Marmarica Formation in the Siwa area includes three members, from bottom to top: the Oasis, Siwa Escarpment, and El Diffa Plateau members. The microfacies of the Marmarica Formation comprise abundant mud‐supported microfacies with minor grain‐supported microfacies. Sedimentation during the Middle Miocene took place on a homoclinal ramp. Dolomitization is the most prevalent diagenetic process that affected carbonate sediments of the Marmarica Formation. The Marmarica Formation comprises two sequence boundaries. The first sequence boundary (SB1) is demarcated by the presence of Thalassinoides ichnofacies at the boundary between the Oasis and Siwa Escarpment members in all the studied sections. It is considered a type 1 sequence boundary. The second sequence boundary (SB2) is represented by an erosional surface, which is recorded only in Girba section. The SB2 was traced at both Naqb El‐Migahhiz and Umm Hiyus sections by the occurrence of burrows that relate to the Glossifungites ichnofacies. The latter boundary is considered type 2. Three third‐order depositional sequences have been recognized in the Middle Miocene Marmarica Formation. Therefore, the Marmarica Formation at Siwa Oasis exhibits relative sea‐level oscillation. During the Middle Miocene, the prevailing warm climate caused transgression and deposition of carbonates along the marine shelf surrounding western and northern Africa.