Reservoir and pumped hydro storage facilities represent one of the best options for providing flexibility at low marginal cost and very low life cycle carbon emissions. However, hydropower generation is subject to physical, environmental and regulatory constraints, which introduce complexity in the modelling of hydropower in the context of transition energy analysis. In this article, a probabilistic model for hydropower generation is developed in order to improve an hourly-resolved tool for transition path analysis presented in previous research. The model is based on time series analysis, which exploits the fact that the different constraints affecting hydropower generation were met in the past. The upgraded version of the transition path analysis tool shows a decrease in the hydropower flexibility as compared with previous published results, providing a better picture of the benefits and drawbacks associated with a specific transition path under analysis, for example in terms of assessing the probability of unserved energy. The upgraded version of the tool was employed to analyse the Spanish National Energy and Climate Plan (NECP), finding consistence between proposals associated with the power system and related CO2 reduction and share of renewable electricity targets.