We determined physiological and morphological responses of the seagrass Cymo docea nodosa and associated epiphytes and epifauna to water column nutrient enrichment, and investigated whether responses were modulated by the clonal integration of the seagrass. Nutrient levels were elevated, relative to 'ambient' plots, in 'large' (similar to 10 to 100x) and 'moderate' (similar to 5 to 10x) enrichment plots, in a seagrass meadow off the south coast of Gran Canaria. Clonal integration was severed in half the plots, isolating them from adjacent shoots. Seagrass shoot density, above-ground biomass and leaf surface were lower in fertilized than ambient plots when clonal integration was severed. In the plots where clonal integration was maintained, no differences in shoot density were observed between fertilized and ambient plots, while differences in above-ground biomass and leaf surface were exclusively observed between 'large' enrichment and 'ambient' plots. Seagrass above-ground tissues accumulated P, but not N, when clonal integration was maintained. The N content, but not P content, of below-ground parts increased with fertilization. The content of soluble sugars in seagrass tissues decreased under nutrient enrichment; this decay was, however, buffered when clonal integration was maintained. Grazing bites on leaves increased with nutrient enrichment regardless of the clonal integration. Epiphytic loads increased at elevated nutrient levels irrespective of the clonal integration. The abundance and richness of epifauna were larger on 'moderate' relative to 'ambient' and 'large' enrichment plots, independently of clonal integration. In conclusion, while the physiological and morphological responses of C. nodosa to nutrient enrichment depended on the maintenance of clonal integration, flow-on effects on epiphytes and epifauna were independent of the clonal integration of the seagrass.