Dead storage of reservoir usually designed by soil erosion rate of catchment area result in certain year without considering land use and precipitation dynamic in the catchment and sedimentation distribution analysis at the bottom of the reservoir as well. Development of protocol is needed for more accurate prediction of reservoir sediment transport to describe the real condition and accommodate data limitations. It will give good perspective in design, operation and maintenance strategy for reservoir. The proposed protocol is consisted of long-term soil erosion prediction, modelling long-term sediment discharge, modelling spatial-temporal reservoir sediment transport and predicting reservoir sediment volume and distribution in the future. The case study is in Wonogiri reservoir, Indonesia. Simulation of the proposed protocol at the case study began by obtaining long-term soil erosion prediction from 1993 – 2019. Sediment discharge was modelled from soil erosion and synthetic long-term hydrographs using the FJ Mock method and validated with sediment rate measured directly in the field. Reservoir sediment transport model was using MIKE software. The simulation gives volume and distribution of sedimentation validated by bathymetry result of the reservoir. Prediction of future sedimentation was using the modular regression method. This protocol promotes spatial reservoir sediment transport model and sedimentation prediction by modular regression. The prediction result of reservoir sediment volume in 2069 is 146.7 million m3. © (2024), (International Journal of Technology). All rights reserved.