Marine phytoplankton and zooplankton form the basis of the ocean’s food-web, yet the impacts of climate change on their biodiversity are poorly understood. Here, we use an ensemble of species distribution models for a total of 336 phytoplankton and 524 zooplankton species to determine their present and future habitat suitability patterns. For the end of this century, under a high emission scenario, we find an overall increase in plankton species richness driven by ocean warming, and a poleward shift of the species’ distributions at a median speed of 35 km/decade. Phytoplankton species richness is projected to increase by more than 16% over most regions except for the Arctic Ocean. In contrast, zooplankton richness is projected to slightly decline in the tropics, but to increase strongly in temperate to subpolar latitudes. In these latitudes, nearly 40% of the phytoplankton and zooplankton assemblages are replaced by poleward shifting species. This implies that climate change threatens the contribution of plankton communities to plankton-mediated ecosystem services such as biological carbon sequestration.

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Shelled pteropods and planktic foraminifers are calcifying zooplankton that contribute to the biological carbon pump via the sinking of their calcareous shells. However, their importance for regional and global plankton biomass and carbon fluxes is not well understood. Here, we modeled global annual patterns of pteropod and foraminifer total carbon (TC) biomass and total inorganic carbon (TIC) export fluxes over the top 200 m using five species distribution models (SDMs). An extended version of the MARine Ecosystem DATa (MAREDAT) of zooplankton abundance observations was used to estimate the biomass of both plankton groups. We found hotspots of mean annual pteropod biomass in the high Northern latitudes and the global upwelling systems, and in the high latitudes of both hemispheres and the tropics for foraminifers. This largely agrees with previously observed distributions. For both groups, temperature is the strongest environmental correlate, followed by chlorophyll‐a. We found mean annual standing stocks of 52 Tg TC (48 to 57 Tg TC) and 0.9 Tg TC (0.6 to 1.1 Tg TC) for pteropods and foraminifers, respectively. This translates to mean annual TIC fluxes of 14 Tg TIC yr−1 (9 to 22 Tg TIC yr−1) for pteropod shells and 11 Tg TIC yr−1 (3 to 27 Tg TIC yr−1) for foraminifer tests. These results are similar to previous estimates for foraminifers, but approximately a factor of ten lower for pteropods. Pteropods contribute 0.2%–3.2% and foraminifers 0.1%–3.8% to global surface carbonate fluxes. Including global coccolithophore fluxes, this leaves 40%–60% of the global carbonate fluxes unaccounted for. Our figures are likely lower‐bound estimates due to sampling data characteristics and uncertainty associated with organism growth rates.

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