Two stratigraphic sections of the Hamam Formation (Bathonian Stage, Middle Jurassic) exposed in the western part of Wadi Zarqa region, northwestern Jordan, are described and interpreted on the basis of palynoflora and facies analysis in order to reconstruct their depositional environments and sequence stratigraphic framework, which not discussed before. Five facies associations have been identified in the Hamam Formation characterized by a mixed carbonate–siliciclastic ramp setting, ranging from incised fluvial valley fill facies, beach foreshore restricted inner ramp to high-energy shoals and mid-ramp settings. The palynoflora includes well-preserved miospore assemblages which are recorded only from the incised fluvial valley fill facies for the first time and yielded 64 miospore species belonging to 40 genera. Most of these taxa are long-ranging and have been reported from Jurassic and Cretaceous rocks worldwide, except Callialasporites dampieri, Murospora florida, Granulatisporites jurassicus, Piceites expositus, Pityosporites parvisaccatus, Leptolepidites verrucatus, and Protopinus scanicus which have short ranges in the Middle Jurassic. Furthermore, these rocks are rich in shallow-marine Neo-Tethys macro-invertebrates supporting a Bathonian age. Two third-order depositional sequences bounded by three regional unconformities at the Bajocian–Bathonian and Bathonian–Callovian stage boundaries as well as within the Bathonian are defined based upon facies characteristics and stratal geometries. A regional correlation of sequence boundaries of similar age indicates that they are eustatic in origin.