Gravitational sinking of photosynthetically fixed particulate organic carbon (POC) constitutes a key component of the biological carbon pump. The fraction of POC leaving the surface ocean depends on POC sinking velocity (SV) and remineralization rate (C_remin), both of which depend on plankton community structure. However, the key drivers in plankton communities controlling SV and C_remin are poorly constrained. In fall 2014, we conducted a 6‐week mesocosm experiment in the subtropical NE Atlantic Ocean to study the influence of plankton community structure on SV and C_remin. Oligotrophic conditions prevailed for the first 3 weeks, until nutrient‐rich deep water injected into all mesocosms stimulated diatom blooms. SV declined steadily over the course of the experiment due to decreasing CaCO₃ ballast and—according to an optical proxy proposed herein—due to increasing aggregate porosity mostly during an aggregation event after the diatom bloom. Furthermore, SV was positively correlated with the contribution of picophytoplankton to the total phytoplankton biomass. C_remin was highest during a Synechococcus bloom under oligotrophic conditions and in some mesocosms during the diatom bloom after the deep water addition, while it was particularly low during harmful algal blooms. The temporal changes were considerably larger in C_remin (max. fifteenfold) than in SV (max. threefold). Accordingly, estimated POC transfer efficiency to 1,000 m was mainly dependent on how the plankton community structure affected C_remin. Our approach revealed key players and interactions in the plankton food web influencing POC export efficiency thereby improving our mechanistic understanding of the biological carbon pump.