This dataset includes counts of organic-walled dinoflagellate cysts identified in 31 surface sediment samples (sampled with a Van Veen grab sampler and a corer device) collected along the Ría de Vigo (NW Iberia). Other relevant data, such as dry weight of processed sample, number of Lycopodium spores added and the Lycopodium spores counted per sample, are also reported. Samples were taken at different depths (from the intertidal to a max. depth of 41 m in the subtidal) during different campaigns between 2006 and 2014. Sediment samples were processed at the Palynology and Palaeobotany Laboratory, at the University of Vigo (Spain), using the standard palynological extraction procedures that included oven drying, treatment with HCl and HF at room temperature, the addition of exotic markers (Lycopodium spores) for concentration estimates and sieving to remove coarse (> 120 µm) and fine (< 10 µm) materials. Cysts were counted under a light microscope (Nikon Eclipse 50i and Olympus BX50) using 400× and 600× magnifications (1000× for critical determinations). The interpretation of cyst distribution in relation to environmental gradients can be found in García-Moreiras et al. (2023).