This study analyses the short-run hydro generation scheduling for the wind power differences from the contracted schedule. The approach for construction of the joint short-run marginal cost curve for the hydro-wind coordinated generation is proposed and applied on the real example. This joint short-run marginal cost (SRMC) curve is important for its participation in the energy markets and for economic feasibility assessment of such coordination. The approach credibly describes the short-run marginal costs which this coordination bears in “real life”. The approach is based on the duality framework of a convex programming and as a novelty combines the shadow price of risk mitigation capability and the water shadow price. The proposed approach is formulated as a stochastic linear program and tested on the case of the Vinodol hydropower system and the wind farm Vrataruša in Croatia. The result of the case study is a family of 24 joint short-run marginal cost curves.