Sediment and nutrients yields especially from farmlands were studied in a watershed in Ishigaki island, Okinawa, Japan. The transport processes of these materials in rivers, mangrove, lagoon and coastal zones were studied by using various observation methods including stable isotope analysis. They were simulated by using a WEPP model which was modified to be applicable to such small islands by identifying several factors from the observations. The model predicts that a proper combination of civil engineering countermeasure and change of farming method can reduce the sediment yield from the watershed by 74%. Observations of water quality and coral recruitment test in Nagura bay indicate that the water is eutrophicated and the corals cannot grow for a long time. Based on these observations, a quantitative target of the reduction of sediment and nutrients yield in watershed can be decided rationally.