Biodiversity losses in marine, terrestrial, and freshwater ecosystems have raised concerns about the maintenance of sustainable ecosystem functions and services ("biodiversity crisis"). A positive diversity-productivity relationship has previously been supported by theoretical models, and by laboratory and field experiments in a variety of ecosystems including unicellular microbial communities. Here we show an increasing biomass yield of aquatic primary producers at the ecosystem scale, paralleled by a long-term positive biodiversity change, which contrasts with the trend of global biodiversity loss. The implied direct long-term biodiversity effect on ecosystem functioning was an increase of phytoplankton biomass per unit limiting nutrient by a factor of 1.2 to 1.4. Changes in diversity of microorganisms may have immediate implications for essential ecosystem processes like productivity and biomass yield. Diversity-driven enhancement of resource use in primary production can lead to increased food web yields, but they also can cause a stoichiometric mismatch between autotrophs and primary consumers. Unveiling the functional roles of planktonic biodiversity therefore has essential implications both for global change and for harvestable marine resources.