The data set compiles biogeochemical water column collected during a KOSMOS mesocosm experiment carried out in the frame work of the Ocean Artificial Upwelling project. The experiment was performed in the North-East Atlantic Ocean off the coast of Gran Canaria in autumn 2018 and lasted for 39 days. In this study we investigated the effect of different intensities of artificial upwelling combined with two upwelling modes (recurring additions versus one singular addition) on POC export and its potential transfer efficiency to depth. The data set includes the amounts of surface water that were exchanged with nutrient-rich deep water (from ~300 m depth), primary production and chlorophyll a, elemental composition of suspended particulate matter (POC, PON, C:N) and prokaryotic heterotrophic production.