Export data from the mesocosm experiment conducted in the Canary Islands in autumn 2019. Sinking matter was collected in 2-days intervals over the course of 33 days from the mesocosm sediment traps (4 m depth). Sediment samples were processed and subsampled for duplicate measurements of particulate organic carbon (POC), nitrogen (PON), phosphorus (POP) and biogenic silica (BSi). Elemental mass fluxes in µmol L-1 were calculated by normalizing to the mesocosm volume. They were then either normalized to the time between sample collection (48 h) to obtain daily mass fluxes (µmol L-1 d-1), or added up to obtain cumulative mass fluxes (µmol L-1). Another set of sediment subsamples was analyzed for particle sinking velocities, sizes and porosities (bidaily) and microbial remineralization rates (every 4 days).