For establishment of adequate environmental, oceanographic and climatic reconstructions based on fossil dinoflagellate cysts associations detailed information on selective transport and preservation is required. Here we present a comparison of export rain of dinoflagellate cysts with cyst associations in different intermediate nepheloid layers in the water column, the bottom nepheloid layer and surface sediments collected along two onshore-offshore transects off Cape Blanc (NW Africa) during active upwelling in November 2015. Highest cyst export production took place at the rim of a newly formed upwelling eddy/filament. Lateral transport of cysts up to 130 km off the shelf break was observed in a nepheloid layer varying in depth of 600 - 1300 m (shelf break - deep ocean) and in the bottom nepheloid layer. No indication of lateral transport could be documented in a second intermediate nepheloid layer deeper in the water column as well as in the more offshore part of the bottom nepheloid layer. The effects of lateral transport as registered from the water column was not reflected in underlying sediments. Selective degradation altering the cyst associations was not observed in the water column but the surface sediment cyst association differed considerable from that of the nepholoid layers and the upper water column. Comparison with long term sediment trap time series of cyst production in the region indicate that the surface samples are modified predominantly by species specific post depositional degradation rather than inter-annual variation in transport and/or production of cysts.