The electrochemical reduction of atmospheric CO$_2$ into high-energy molecules with renewable energy is a promising avenue for energy storage that can take advantage of existing infrastructure especially in areas where sustainable alternatives to fossil fuels do not exist. Automated laboratories are currently being developed and used to optimize the composition and operating conditions of gas diffusion electrodes (GDEs), the device in which this reaction takes place. Improving the efficiency of GDEs is crucial for this technology to become viable. Here we present a modeling framework to efficiently explore the high-dimensional parameter space of GDE designs in an active learning context. At the core of the framework is an uncertainty-aware physics model calibrated with experimental data. The model has the flexibility to capture various input parameter spaces and any carbon products which can be modeled with Tafel kinetics. It is interpretable, and a Gaussian process layer can capture deviations of real data from the function space of the physical model itself. We deploy the model in a simulated active learning setup with real electrochemical data gathered by the AdaCarbon automated laboratory and show that it can be used to efficiently traverse the multi-dimensional parameter space.