The Suape Industrial Port Complex is one of the main Brazilian public ports that has caused several geomorphological changes in Ipojuca and Suape estuarine-lagoonal-bays since its construction. The present study deals with the first status on the Suape port ecosystem, recorded from 41 sediment samples throughout the Massangana/Tatuoca and Ipojuca/Merepe estuarine systems. Species diversity values are higher in the seaward part of the bays and decreases toward the inner parts. The dominance of Ammonia tepida in the inner portions of the bays is indicative of environmental instability and pollution of coastal waters. Eggerella spp., unusual in Brazilian fauna, was present only in the innermost portion of the Tatuoca estuary, in the dredged channel, where heavy metal impacts have been reported. Amphistegina gibbosa, Triloculina oblonga, and Quinqueloculina lamarckiana are represented on the outside of the bays and are indicative of high hydrodynamic marine environments. The Ipojuca and Merepe rivers presented the highest ecological index, possibly attributed to the marine and terrestrial/mangrove influence for the region. We infer that geomorphological transformation caused by the Suape Port installation modified and established environments with distinct characteristics, mainly in the Suape Bay dredged area, indicative of possible eutrophication of this environment. The new data may be useful for determining environmental conditions and establishing new ways to monitor the consequences of anthropogenic interference and dredging in the Massangana/Tatuoca and Ipojuca/Merepe estuarine systems.