This dataset contains foraminiferal assemblages from sediment cores collected in the Trunvel and Kerallé valleys, Brittany, North-West France. These analyses were carried out as part of the doctoral project Paleogeographic changes and coastal archaeological remains in Brittany during the Middle and Late Holocene: Contributions of a multidisciplinary and multi-scaled approach, with the aim of reconstructing the Holocene evolution of small estuarine systems on the North-West French coast. The foraminifera content was analyzed in 118 samples to characterize estuary-type deposits. Approximately 300 specimens were systematically identified within the 63-315 μm fractions to obtain a statistically representative result. The relative abundance was expressed as a percentage of the total population.