Here we developed and validated a new Benthic Foraminiferal Salinity (BFS) index from marginal-marine environments by analysing benthic foraminifera from the Holocene Guadalquivir estuary sediments (SW Spain). This index is formulated utilising only four species: Ammonia tepida and Haynesina germanica with higher tolerance to brackish waters and indicating lower salinity, and Elphidium translucens and Elphidium granosum indicative of greater marine influence and pointing to higher salinity. Thus, the BFS index is calculated easily and rapidly, and therefore it makes it possible to analyse a higher number of samples in less time. The BFS index values from the studied cores enabled the detailed description of subtle changes in the Guadalquivir estuary restriction during the Holocene. For this purpose, three degrees of salinity, depending on marine influence, were defined: higher (BFS index = 0.0-0.4, high marine influence), moderate (BFS index = 0.4-0.7, moderate marine influence), and lower (BFS index = 0.7-1.0, low marine influence). Before 2000 BCE, the estuary was moderately open and well-connected to the Atlantic Ocean. From 2000 BCE, the estuary experienced a greater marine influence, increasing in extension, as a consequence of a sea-level rise and subsidence. Immediately afterwards, it began to experience restriction processes due to southward shoreline progradation related to the growth of littoral spits and sediment supply. From 1400 to 1000 BCE, gradual restriction transformed the open estuary into a semiclosed estuary. A last phase of estuary restriction occurred from 1000 BCE to the present day, leading to the lowest salinity and the highest estuary restriction. Finally, the BFS index was successfully applied in two other marginal-marine environments: a Pleistocene lagoon in northern Italy, and a Pliocene coastal bay in southeastern Spain. The index allowed assessment of the degree of restriction in these different environments, supporting its utility in different regions, environments and timescales.