Two internationally important Ramsar lagoons on the south coast of the Caspian Sea (CS) have been studied by palynology on short sediment cores for palaeoenvironmental and palaeoclimatic investigations. The sites lie within a small area of very high precipitation in a region that is otherwise dry. Vegetation surveys and geomorphological investigations have been used to provide a background to a multidisciplinary interpretation of the two sequences covering the last four centuries. In the small lagoon of Amirkola, the dense alder forested wetland has been briefly disturbed by fire, followed by the expansion of rice paddies from AD1720 to 1800. On the contrary, the terrestrial vegetation reflecting the diversity of the Hyrcanian vegetation around the lagoon of Anzali remained fairly complacent over time. The dinocyst and non-pollen palynomorph assemblages, revealing changes that have occurred in water salinity and water levels, indicate a high stand during the late Little Ice Age (LIA), from AD <1620 to 1800–1830. In Amirkola, the lagoon spit remained intact over time, whereas in Anzali it broke into barrier islands during the late LIA, which merged into a spit during the subsequent sea level drop. A high population density and infrastructure prevented renewed breaking up of the spit when sea level reached its maximum (AD1995). Similar to other sites in the region around the southern CS, these two lagoonal investigations indicate that the LIA had a higher sea level as a result of more rainfall in the drainage basin of the CS.