Abstract Seagrass recovery has been reported across the globe where previously eutrophied waters have become less nutrient‐rich. In the European Wadden Sea, different recovery trajectories were found after riverine nutrient loads decreased, namely full, temporary and no recovery. We compiled intertidal seagrass presence (Zostera noltei and Z. marina) and eutrophication data for 1930–2020, to relate the seagrass trajectories and regional eutrophication differences to riverine nutrient loads, and inferred prospects for seagrass recovery. Seagrass fully recovered in the less eutrophic North Frisian region. The recovery trajectory was tightly coupled to riverine nutrient load reduction. Relative seagrass area (meadow area/region area) dropped from 10% prior to eutrophication to 2% during the eutrophication peak, increased to 7% during the nutrient reduction period and subsequently expanded to 13%. Colonization of marginal habitats was observed, indicating propagule spillover from neighbouring meadows. The more eutrophic southern regions showed no or only temporary seagrass recovery. Prospects for (limited) recovery are good in only two out of four southern regions, provided that riverine nutrient loads are further reduced by ~40% (reference: 2010–2017). Without this reduction, seagrasses may only temporarily recover and will remain vulnerable to erratic disturbances like macroalgae accumulation or storms. Historical evidence and application of habitat suitability models suggest that the potential relative seagrass area in the southern regions is low: less than 0.2% in the western Dutch region and maximum 2.4% in the Ems‐Jade region. Synthesis and applications. Within a large seascape (15,000 km2) the least eutrophicated region showed seagrass recovery upon nutrient reduction. We translated the critical riverine nutrient loads for this recovery, via regional eutrophication indicators, to loads that may enable a sustained recovery in the other regions. This technique is applicable in other complex systems, provided sufficient historical data are available. Propagule spillover exerts a positive feedback at metapopulation scale leading to acceleration of recovery. Occupied and potential seagrass habitat (e.g. assessed by the maximum recorded area in the past) are thus important landscape selection criteria for restoration, particularly when eutrophication is not yet sufficiently reduced.