This study is about 3D Numerical Investigation of Settling basin layout by using numerical modeling program SSIIM. This study is carried out by using SSIIM windows version 1 (SSIIM 1.0). SSIIM is numerical modeling software, developed at NTNU by Professor Nils Reidar B. Olsen. This program has been used for investigation numerical modeling of hydraulic and sediment transport for different layouts geometry of settling basin.In this study a case study has carried out on settling basin layout of Mai Khola Hydropower Project, Nepal. Hydraulics performance of proposed layout and one alternative layout with shorter approach is numerically investigated by water and sediment flow computation. For the Numerical investigation structured grid for settling basin layout has developed with the help of drawing provided and excel spread sheet program. Hydraulics performance is investigated for design discharge with constant flow. The hydraulic performance of closing of one chamber and operation of remaining chamber with design discharge of power plant is also investigated. Based on water flow computation result, sediment computation was carried out for one settling chamber, proposed, alternative and modifications of proposed layouts. Effect of approach geometry on distribution of sediment on four chambers of settling basin and sediment trap performance were studied by sediment flow simulation. Effects of closing of chamber on distribution of sediment concentration were also investigated with the help of sediment simulation. Trapping efficiency is evaluated for one settling chamber, proposed alternative and modification layouts and closing mode models. Trap efficiency of one settling chamber model is compared with trap efficiency by analytical method.Based on hydraulic performance, sediment distribution performance and trap efficiency performance; recommendation of modification on approach geometry has made. Also, studied result shows that SSIIM 1.0 version can be used for investigating performance of hydraulic structures and settling basin.