This study tested the hypothesis that sea bottom characteristics interact with light attenuation in the water column to regulate the depth limit of eelgrass Zostera marina L. A large-scale field data set on eelgrass depth limits, light climate and physico-chemical sea bottom characteristics was collected from Danish coastal waters and analyzed by statistical models. The results confirmed that light attenuation is the main predictor of eelgrass depth limits, but indicated that sediments characteristic of eutrophic conditions and physically protected environments also play a regulating role. Depth limits were moderately shallower when the sea bottom was rich in organic material, had high concentrations of nutrients and hydrogen sulfide, and had a physical structure characterized by fine particles, high porosity, high water content and low density. The effect of sediment variables was non-linear, and the sediment only affected depth limits beyond certain threshold levels characteristic of eutrophic conditions and physically protected environments. We argue that further reductions in nutrient loads can improve the state of eelgrass beds by ameliorating not only light conditions but also sediment quality and associated oxygen concentrations in the water column.