Seaweed farming is often depicted as a sustainable form of aquaculture, but suspected habitat alterations and spread of algae outside farms have rendered speculations on the actual degree of sustainability. We conducted an experimental field study on Unguja Island (Zanzibar, Tanzania) to investigate the effects of off-bottom seaweed farming on a tropical seagrass ecosystem, using 1.5 × 2.5 m experimental farm plots. After 11 wk, above-ground seagrass biomass was 40% lower than in control plots, owing to a combination of lower shoot density, shoot length and leaf growth rate. Since the biomass was constant between Day 15 and 75 in the farm (F) treatment, but increased by 67 vs. 48% in the 2 controls (control treatment [C] and stick-and-line control treatment [CSL]), the effect exerted by the farm was a lack of potential biomass increase rather than an actual decrease. The effect was transplanted to associated organisms both in terms of lower seagrass epiphyte cover and changes in the abundance of 2 dominating epifauna taxa (>1 cm): sea urchins and sponges. Furthermore, the F treatment caused an accumulation of seagrass leaf litter, but did not affect sediment organic matter (SOM) content. The mechanisms behind these effects were not explicitly tested, but algal shading, emergence stress and mechanical abrasion were identified as likely contributors. Interestingly, the effects were largely restricted to 1 of the 2 seagrass species present, Enhalus acoroides, while the other, Thalassia hemprichii, remained more or less unaffected. This may be due to reduced interspecific competition or species-specific differences in morphology and stress tolerance, and could in the long-term have implications for (amongst others) associated fish communities. Although seaweed farming at the current level is less detrimental than, for example, intensive shrimp farming, and therefore should be seen as a strong option for future aquaculture developments, intensive farming on seagrasses should be avoided or at least minimized by, for example, implementing other farming methods. The risk of ecosystem-level changes in large-scale and uncontrolled farm enterprises warrants a holistic and integrated coastal management approach which considers all aspects of the tropical seascape including human societies and natural resource use.