Seed represents a potentially ecologically sustainable source of planting units for restoring seagrasses, particularly for seagrasses where transplanting negatively impacts donor beds. However, newly germinated seeds may be nutrient limited as their underdeveloped root systems may constrain capacity to access sediment-based resources. We conducted a study in land-based aquaculture tanks to determine whether early growth of newly germinated Posidonia australis seedlings could be enhanced by adding inorganic nutrients to the sediment. Sediments were supplemented with nitrogen and phosphorus in a factorial design (no nutrients, N, P, N + P). Shoot survival, whole shoot biomass, root morphology, root architecture, and nutrient concentration of seedlings were assessed monthly for the first 4 months after germination. More than 90% of seedlings survived during the 4 months of the experiment, irrespective of nutrient treatment. Growth of P. australis seedlings was not enhanced by addition of N or P to the sediment despite nutrient uptake occurring. Seedling growth was found to be more dependent on seed nutrient reserves rather than external nutrient sources for at least the first 4 months after germination. Adding inorganic nutrients to the sediment also significantly reduced the development of the seedling root system in terms of biomass, length, and density of lateral root branches. This study demonstrated that inorganic nutrient supplements constrain root development and therefore capacity for successful anchorage of seagrass seedlings, and pose a significant limitation on seedling establishment when transferred to the field, as well as potentially limiting natural and transplanted seedling establishment in eutrophic sediments.