In this study, two hydrologic models, the Gridded Surface Subsurface Hydrologic Analysis (GSSHA) and the Soil and Water Assessment Tool (SWAT), were applied to predict stream flow and suspended sediment concentration (SSC) in a small agricultural watershed in Ishigaki Island, Japan, in which the typical time scale of flood event was several hours. The performances of these two models were compared in order to select the right model for the study watershed. Both models were calibrated and validated against hourly stream flow and SSC for half-month periods of 15 to 31 May 2011 and 17 March to 7 April 2013, respectively. The results showed that both models successfully estimated hourly stream flow and SSC in a satisfactory way. For the short-term simulations, the GSSHA model performed slightly better in simulating stream flow as compared to SWAT during both calibration and validation periods. GSSHA only gave better accuracy when predicting SSC during calibration, while SWAT performed slightly better during validation. For long-term simulations, both models yielded comparable results for long-term stream flow and SSC with acceptable agreement. However, SWAT predicted the overall variation of long-term SSC better than GSSHA.