To extend the understanding of dinoflagellate cysts production, excystment and vertical/lateral transport in the water column, we compared upper water cyst export production with cysts associations and concentrations in the subsurface nepheloid layer, bottom nepheloid layer and deeper water column during active upwelling off Cape Blanc (NW Africa) in August 2020. Export production was collected by two drifting trap surveys; DTS1 in an active upwelling cell for 4 days and DTS2 in an offshore drifting upwelling filament for 2 days. Subsurface, bottom nepheloid layers and deeper waters were sampled by in-situ pumps along two transects perpendicular to the shelf break. During DTS1, light limitation hampered phytoplankton production which might have influenced cyst production negatively due to up- and downward movement of water masses. Cyst export production increased at the rim of the upwelling cell. For DTS2, upwelling filament cyst export production was up to 3 times lower than that of DTS1. Echinidinium delicatum had highest relative and absolute abundances in the active upwelling, Echinidinium zonneveldiae and Bitectatodinium spongium in the upwelling filament, and Impagidinium spp. and cysts of Gymnodinium microreticulatum/nolleri at the most distal stations. Comparison of concentrations of cysts with and without cell contents showed that the majority of cysts hatched before reaching deeper waters and displayed a dormancy period of less than 6 days. About 5% of the living cysts reached deeper waters and/or the ocean floor. Living cysts were transported offshore in the upwelling filament. In case ships exchange ballast waters in the studied region, they will take up laterally transported living cysts. Upon release of the ballast waters in the port of arrival, these cysts have the potential to become “invader species” that can threaten economy and/or health. Lateral transport of cysts was observed in the bottom nepheloid layer and in deeper waters (800 - 1200m depth) with a maximal extension of about 130km off the shelf break. Therefore, sediments in the region will contain a mixture of regionally and locally produced dinoflagellate cysts. This insight contributes to the improvement of environmental reconstructions of the Cape blanc upwelling system based on downcore cyst associations.