Coral reefs which are an important resource to coastal communities and nation at large are adversely affected by rate of sediment flux to the reefs. However, there is little information on seasonal trend in sediment flux and its impact at the reefs off Zanzibar. Two years’ monthly data on sedimentation at Chumbe and Bawe reefs were used to assess seasonal variability in sediment flux and its implication on the coral status. Sediment flux to the Bawe reefs for the duration of the study ranged from 0.2 to 41.5 mg cm 2 d 1, while it ranged from 0.8 to 65.8 mg cm 2 d 1 at the Chumbe reefs. Sediment fluxes at Bawe reefs were highest between November and March, while they were highest between April and September at Chumbe reefs. Generally, sediment fluxes at Bawe reefs were low compared to those at Chumbe. The total sediment input to the reefs ranged from 4615 to 123,403 kg d 1 for Bawe reefs and 2750 to 79,636 kg d 1 for Chumbe reefs. High sediment fluxes at Bawe reefs between November and March; and the Chumbe reefs between April and September can be attributed to water currents and wind pattern in the east African region which are under the influence of the monsoons. The observed trend suggests that the period for coral transplant as a management option for the two sites should be different. Coral transplant can be undertaken in such a way that stress of the corals due to sedimentation can be felt after they have overcome stress from transplant process and temperature. The results from this study contribute to the much needed information for coral transplant, restoration, and management