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Global change causes fluctuations as rainfall deficits that in some cases amplifies the reduction in nutrient intakes required for water quality regulation. In this context, oligotrophication reduces the pelagic production of coastal ecosystems and promotes the return of benthic macrophytes such as Zostera meadows. It is now necessary to know and understand the potential benefits related to the return of seagrass beds associated with the environmental recovery of shellfish-exploited-ecosystems (SEE). The French–Japanese SAKURA project aimed to (1) clarify and compare relationships between dynamics of nutrient levels, phytoplankton, and oyster production in the Thau Lagoon (France) and Hiroshima and Aki bays, using historical data analysis and carrying capacity models, (2) highlight the Zostera spp. contribution to oyster life cycles studying the variability of larval recruitment, survival, growth of juveniles, and trophic regime of oysters in the presence or in the absence of Zostera spp. meadows, (3) describe and compare the dynamics of socio-ecosystems of SEE under oligotrophication. First results of the SAKURA project permitted to start to improve knowledge on the influence of oligotrophication processes on the ecological status of shellfish-exploited-ecosystems and on the oyster life cycle. Analysis is still ongoing. Now, the French and Japanese partners want to deepen the interdisciplinary approach and the knowledge of this major sea and coastal challenge by expanding their partnership in the international community to address more holistically the conservation of biodiversity and the sustainable use of resources in the changing coastal seas.