To evaluate whether proxies that record surface, near-surface, and bottom water conditions from the North Iceland shelf have similar trends and periodicities, we examine Holocene century-scale paleoceanographic records from core MD99-2269. This core site lies close to the boundary between Atlantic and Arctic/Polar waters, and in an area frequently influenced by drift ice. The proxies are stable δ13C and δ18O values on planktonic and benthic foraminifera, alkenone-based sea-surface temperatures (SST°C), and foraminiferal Mg/Ca SST°C and bottom water temperature (BWT°C) estimates. These data were converted to equi-spaced 60-year time-series; significant trends were extracted using Singular Spectrum Analysis, which accounted for between 50% and 70% of the variance. In order to evaluate within-site ocean climate variability, a comparison between these data and previously published proxies from MD99-2269 was carried out on a standardized data set of 14 proxies covering the interval 400–9200 cal. yr BP. Principal component (PC) analysis indicated that the first two PC axes accounted for 57% of the variability with high loadings primarily defining ‘nutrient’ and ‘temperature’ proxies. Fuzzy k-mean clustering of the 14 climate proxies indicated major environmental changes at ~6350 and ~3450 cal. yr BP, which define local early-, middle-, and late-Holocene climatic shifts. Our results indicate that the major control on the combined proxy signal is the Holocene decrease in June insolation, but regional changes in such factors as sea-ice extent and salinity are required to explain the threefold division of the Holocene.