Seagrass beds are globally declining due to human activities in coastal areas. We here aimed to identify threats from eutrophication to the valuable seagrass beds of Curaçao and Bonaire in the Caribbean, which function as nursery habitats for commercial fish species. We documented surface- and porewater nutrient concentrations, and seagrass nutrient concentrations in 6 bays varying in nutrient loads. Water measurements only provided a momentary snapshot, due to timing, tidal stage, etc., but Thalassia testudinum nutrient concentrations indicated long-term nutrient loads. Nutrient levels in most bays did not raise any concern, but high leaf % P values of Thalassia in Piscadera Bay (0.31%) and Spanish Water Bay (0.21%) showed that seagrasses may be threatened by eutrophication, due to emergency overflow of waste water and coastal housing. We thus showed that seagrasses may be threatened and measures should be taken to prevent loss of these important nursery areas due to eutrophication.