Knowledge of the variability of Atlantic water inflow is critical for understanding the hydrography and ecology of the northern North Sea. However, long term records of this variability, which can be used to refine model projections of future environmental change in the region, are limited. The Fetlar Basin, located to the east of the Shetland Islands (UK), is a depositional basin situated at the intersection of the North Atlantic and northern North Sea, making it ideally placed for studying variability in Atlantic inflow. Datasets have been generated from a marine sediment core spanning the Late glacial and Holocene (c. 13 k cal a BP to present), including benthic foraminiferal assemblages, stable isotopes (δ18O and δ13C of Quinqueloculina seminulum), grain size, and sediment total organic carbon. Cluster and principal component analyses of benthic foraminiferal assemblages enabled the definition of five foraminiferal zones. The two basal zones (c. 12.9–11.0 k cal a BP) contain cold water, sea ice and glaci-proximal species typical of the Late glacial, as well as high abundances of juvenile forms. A transition from cool to warmer Holocene conditions occurs from c. 11.5 k cal a BP in a well-mixed water column. During the mid Holocene, high abundances of F. fusiformis are coincident with lower δ18O. These coincide with the Mid Holocene Climatic Optimum, and or indicate fresher, more nutrient rich water associated with higher contributions of Modified North Atlantic Water in relation to an expansion of the subpolar gyre. From c. 4.2 k cal a BP to the present, foraminiferal δ18O values indicate cooler and potentially more saline conditions, which align with a general late Holocene cooling pattern in Northern Europe, and or increasing salinity due to a retraction of the subpolar gyre. Our findings provide potential long-term evidence for recent studies which emphasize the role of subpolar gyre variability in regulating North and Norwegian Sea salinity. This variability should thus be considered in the modelling and management of this region.