We present an SiF4 separation line, coupled to a laser fluorination system, which allows for an efficient combined silica δ18O and δ30Si analysis (50 min per sample). The required sample weight of 1.5–2.0 mg allows for high-resolution isotope studies on biogenic opal. Besides analytical tests, the new instrumentation set-up was used to analyse two marine diatom fractions (>63 µm, 10–20 µm) with different diatom species compositions extracted from a Bølling/Allerød–Holocene core section [MD01-2416, North-West (NW) Pacific] to evaluate the palaeoceanographic significance of the diatom isotopic signals and to address isotopic effects related to contamination and species-related isotope effects (vital and environmental effects). While δ30Si offsets between the two fractions were not discernible, supporting the absence of species-related silicon isotope effects, systematic offsets occur between the δ18O records. Although small, these offsets point to species-related isotope effects, as bias by contamination can be discarded. The new records strengthen the palaeoceanographic history during the last deglaciation in the NW Pacific characterized by a sequence of events with varying surface water structure and biological productivity. With such palaeoceanographic evolution it becomes unlikely that the observed systematic δ18O offsets signal seasonal temperature variability. This calls for reconsideration of vital effects, generally excluded to affect δ18O measurements. Copyright © 2013 John Wiley & Sons, Ltd.