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Geoarchaeological information presented here pertains to a subsidiary Nile channel that once flowed west of the main Sebennitic distributary and discharged its water and sediments at Egypt’s then north-central deltaic coast. Periodical paleoclimatic episodes during the later Middle and Upper Holocene included decreased rainfall and increased aridity that reduced the Nile’s flow levels and thus likely disrupted nautical transport and anthropogenic activity along this channel. Such changes in this deltaic sector, positioned adjacent to the Levantine Basin in the Eastern Mediterranean, can be attributed to climatic shifts triggered as far as the North Atlantic to the west, and African highland source areas of the Egyptian Nile to the south. Of special interest in a study core recovered along the channel are several sediment sequences without anthropogenic material that are interbedded between strata comprising numerous potsherds. The former are interpreted here as markers of increased regional aridity and reduced Nile flow which could have periodically disrupted the regional distribution of goods and nautical activities. Such times occurred ~5000 years B.P., ~4200–4000 years B.P., ~3200–2800 years B.P., ~2300–2200 years B.P., and more recently. Periods comparable to these are also identified by altered proportions of pollen, isotopic and compositional components in different radiocarbon-dated Holocene cores recovered elsewhere in the Nile delta, the Levantine region to the east and north of Egypt, and in the Faiyum depression south of the delta.