The Iberian Margin, located in the mid-latitude North Atlantic at the western edge of the European continent, is a key region for climate and oceanographic research. The Portuguese western coast marks the northernmost boundary of the Canary Current upwelling system, experiencing seasonal wind-driven coastal upwelling from May to September. Eastern Boundary Upwelling Systems (EBUS) are among the most productive regions in the global ocean. They play a vital role in climate regulation and support both local and global fisheries. As part of the ICW3P project (PTDC/CTA-CLI/2884/2021) 'Impact of climate warming in the coastal upwelling system and primary production off Portugal: a study linking classical and emerging proxies', this study presents multi-proxy records from three inner-shelf sediment sequences. The project aimed to evaluate different nutrient sources and paleoceanographic features of the Iberian Margin and to reconstruct primary productivity and phytoplankton community variability over the past 1,000 years.This dataset presents diatom assemblages from a sediment record where these microfossils are best preserved, collected off the mouth of the Douro River (POS287-06G), in the north-western region of the Portuguese continental shelf, using a gravity coring system during the Poseidon cruise POS287 in 2002. This analysis was conducted at the EMSO-Gold Optical Laboratory at IPMA during 2022 and 2023, using differential phase interference microscopy, Eclipse 80i.