Characterizing the memory properties of the environment has become critical for the high-fidelity control of qubits and other advanced quantum systems. However, current non-Markovian tomography techniques are either limited to discrete superoperators, or they employ machine learning methods, neither of which provide physical insight into the dynamics of the quantum system. To circumvent this limitation, we design learning architectures that explicitly encode physical constraints like the properties of completely-positive trace-preserving maps in a differential form. This method preserves the versatility of the machine learning approach without sacrificing the efficiency and fidelity of traditional parameter estimation methods. Our approach provides the physical interpretability that machine learning and opaque superoperators lack. Moreover, it is aware of the underlying continuous dynamics typically disregarded by superoperator-based tomography. This paradigm paves the way to noise-aware optimal quantum control and opens a path to exploiting the bath as a control and error mitigation resource.