Over the last few years Norway has seen an increasing number of hours where the grid frequency exceeds the required limits (49.9-50.1Hz). To improve this situation one alternative is to implement hydropower governing with quicker response time. However, long conduits and oscillatory flow set strict requirements to the hydropower system stability and turbo set governing. This thesis establishes a simulation program based on the structure matrix method for stability analysis of hydropower systems. The method is implemented in a Matlab program to study the oscillatory flow in the frequency domain. Implementation of frictional influence, turbine characteristics, and alternative governing has been given special attention. The program is validated through comparison with measurements and previous analysis at Kongsvinger and Tafjord power plants. The program simulations generally compare well with physical dynamics of the two systems. Further a stability analysis of speed governing at Aldal power plant has been performed. Finally some alternative control systems are discussed.