This study reconstructs the paleoecological settings of Chilia/Licostomo, the most important Genoese colony in the Danube delta. Our paleoenvironmental data (i.e., sedimentology, pollen, charcoal, radiocarbon ages) corroborate historical and archaeological information over the last seven centuries to document the habitation at Chilia and its military and socioeconomic activity during ca. 14th–19th centuries A.D. Palynological data show the continuous presence of humans, with anthropogenic pollen index calculation (API) values between 2% and 16% during the last five centuries. The variability of API, corroborated with the major peaks of the charcoal concentration, matches the documented military conflicts and population changes in the area: the Ottoman conquest of Dobrugea (15th century A.D.), the Zaporozhians Cossaks raids (17th century A.D.), and the Russian–Ottoman wars (18th–19th centuries A.D.). The presence of coprophilous fungi fits the Ottoman tradition of animal husbandry, whereas their appearance after the Zaporozhians Cossacks raids and their good correlation with open land vegetation suggest that the Chilia loess island was temporally used as a refuge from multiple menaces (e.g., wars, administrative crisis). These paleoecological data, together with the rare archaeological findings, exclude human habitation of the Chilia Plain earlier than the documented arrival of the Lipovans during the late 18th century A.D. The critical assessment of the correspondences between the paleoecological and historical data shows the relevance of the approach in deltaic environments, when applied to lagoon/lacustrine sediments, yet often limited to chronologically disparate, decennial‐ to multicentennial‐scale temporal frameworks.