► A 3D RANS model was used to compute the suspended sediment distribution in a reservoir. ► The study includes 3D measurements of the sediment distribution using a LISST-SL device. ► The measurements were used to validate the numerical model. ► The morphological bed level changes during an entire operation year were simulated. ► The simulations showed good agreement with the measured deposition pattern. The three-dimensional numerical model SSIIM was used to compute suspended sediment distribution and deposition pattern in a hydropower reservoir. The study also included three-dimensional measurements of suspended sediments in the reservoir using the LISST-SL instrument. The measurement device is based on a laser-diffraction method and measures concentrations and grain size distributions instantly. It was applied to 25 locations in the reservoir where vertical profiles were taken. The measurements and computed results were compared and reasonable agreement was found. In addition, computed bed elevation changes were compared with measured values in the conducted study. The results of the numerical model agree well with the bed levels taken by echo sounding. The numerical model SSIIM solves the Reynolds-averaged Navier–Stokes equations in three dimensions and uses an adaptive grid which moves in accordance to changes in the water and bed levels. The suspended sediment transport is calculated by solving the convection–diffusion equation and the bed load transport by an empirical formula. The used implicit free-water surface algorithm provides the possibility of using large time step sizes, which makes a simulation of an operation year on a desktop PC possible.