To understand the effect of rainfall on sediment and nutrient fluxes in a mangrove river ecosystem, field observations were conducted in the Fukido River, Okinawa, Japan. Water currents and water quality parameters (salinity and turbidity) were measured at the river mouth and upstream, and surface water samples were analyzed for nutrient concentrations (NO3-N, NH4-N, PO4-P, SiO2-Si, suspended solids [SS], total nitrogen [TN], and total phosphorus [TP]). Observations were conducted on both clear and rainy days, which revealed the effect of weather. SS flux at the river mouth (outflux to sea) and upstream (influx from land) showed that sediment deposition occurred in the mangrove swamp, and the amount of sediment deposition on a rainy day (324 kg d–1) was approximately 14 times greater than that on a clear day (24 kg d–1). The higher influx from upstream on the rainy day caused levels of TN and TP deposition in the mangrove swamp that were 9.1 and 3.4 times higher, respectively, than levels on a clear day. Our findings highlight the importance of considering local weather conditions in the estimation and management of nutrient budgets, especially in a small mangrove river.