This dataset contains the values of natural abundance of stable measured in 4335 samples of plankton size fractions sampled during the PELACUS spring cruises in the northwestern Iberian shelf and in adjacent waters of the southern Bay of Biscay. Plankton was collected by plankton nets of 30 cm diameter, 40 µm mesh size (fractions 200 µm) by vertical hauls between the surface and 100 m depth (or less if bottom depth <100 m). Final size fractionation was made on board using nylon mesh sieves (20, 40, 53, 80, 200, 500, 1000, 2000, and 5000 µm mesh size). In some cruises surface water was pre-filtered through sieves of 20 or 40 µm mesh-size and subsequently filtered through Whatman glass–fibre GF/F filters. Samples were preserved frozen on board (-20°C) and subsequently oven dried (60°C, 48 h) in the laboratory. No treatments for removing lipids or inorganic carbon were used prior to carbon analyses. Stable isotope determinations in bulk samples (also carbon and nitrogen contents) were made by isotope-ratio mass spectrometry coupled to an elemental analyzer and stable nitrogen isotopes in amino acids were determined by isotope-ratio mass spectrometry coupled to a gas chromatograph (García Seoane et al. 2023).