Due to the coexistence of different gases in underground storage, this work explores the interface stability’s impact on energy storage, specifically during the injection and withdrawal of gases such as hydrogen and natural gas. A new approach of combing simulation and time series analysis is used to accurately predict instability modes in energy systems. Our simulation is based on the 2D Euler equations, solved using a second-order finite volume method with a staggered grid. The solution is validated by comparing them to experimental data and analytical solutions, accurately predicting the instability’s behavior. We use time series analysis and state-of-the-art regime-switching methods to identify critical features of the interface dynamics, providing crucial insights into system optimization and design.