This dataset includes counts, percentages and concentrations of all dinoflagellate cyst taxa identified in the benthic nephloid layer (BNL), cyst rain and surface sediments collected along a land-sea transect off Figueira da Foz (NW Portugal, Atlantic Iberian margin) during the Hydrographic Institute (IH)-HABWAVE cruise (16th-19th September 2019). Sampling of the dinoflagellate cyst community in the BNL, the water column (sediment trap) and the surface sediments (together with studies of spatio-temporal changes in physical properties) were carried out in order to investigate the dinoflagellate cyst distribution and the factors (physical and biological) affecting it. Water samples for cyst analyses were collected by a rosette firing system associated with the CTD, and the cyst rain using a sediment trap situated above the BNL. They were filtered (40-47 l) on board through a 150µm-nylon mesh sieve onto a 10µm-calibrated stainless steel sieve (Retsch). In the laboratory, cysts were concentrated by centrifugation. Full and empty cysts were counted to investigate whether a reservoir of viable cysts existed in the BNL. Surface sediments were sampled with a Smith McIntyre grab and using Plexiglass tubes (3.6 cm internal diameter) that were inserted in the sediment to recover the top 1-cm layer. Cysts from sediments were concentrated by density separation with sodium polytungstate (2.016 g/ml).