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• A multi-proxy approach of late Holocene evolution from Valencia lagoon is presented. • A transition from coastal to fluvial processes shapes the lagoon morphology. • Between 2.8 and 1.2 ka, cold event is registered as a decline in marine influence. • A brackish marsh around 1.2 ka is contemporary with Medieval Climate Optimum. • In the last 0.8 ka, increased fluvial activity in the Little Ice Age is recorded. This study reconstructs the evolution of foraminiferal assemblages and the environmental variables (type of substrate, content in calcium carbonate and content in organic matter) in the Valencia lagoon (western Mediterranean) in response to changes in the late Holocene. In this area of low tidal range, several multiproxy analyses were carried out to determine which environmental variables influence the distribution of the fossil assemblage, and its association with global, regional or local climatic phenomena. The statistical results show that in environments with higher exposure to marine conditions, the calcium carbonate content is the dominant factor, whereas in more restricted environments the type of substrate (grain size) is determinant. The micropaleontological content reveals the evolution from a saline paleoenvironment with a clear marine influence towards the hyposaline or freshwater conditions, recorded at the top. Three phases were identified in the evolution of this area from 2800 cal yr BP to the present. A brackish lagoon with marine connection at the base, followed by a deposit of brackish lagoon (1232 ± 74 cal yr BP − 791 ± 104 cal yr BP), culminating in a brackish marsh (791 ± 104 cal yr BP to present), interpreted as the definitive closure process of the lagoon, favored by the coastal progradation processes related with an extraordinary input of sediments. These findings reflect the climatic variability of the Medieval Climate Optimum (MCO) (1.05 and 0.65 kcal BP) and the migration of the river Turia mouth, which favored the coastal progradation processes. The flood events registered at this phase, may have coincided with changes in the landscape and greater anthropic influence at the end of the LIA, 150 cal yr BP. Coastal processes are mainly responsible for the evolution of this area during phase I, while the influence of fluvial processes is significant towards the top, especially in phase III. [ABSTRACT FROM AUTHOR]