Digital communication systems inherently operate through physical media governed by partial differential equations (PDEs). In this paper, we introduce a physics-aware decoding framework that integrates gradient descent-based error correcting algorithms with PDE-based channel modeling using differentiable PDE solvers. At the core of our approach is gradient flow decoding, which harnesses gradient information directly from the PDE solver to guide the decoding process. We validate our method through numerical experiments on both the heat equation and the nonlinear Schrödinger equation (NLSE), demonstrating significant improvements in decoding performance. The implications of this work extend beyond decoding applications, establishing a new paradigm for physics-aware signal processing that shows promise for various signal detection and signal recovery tasks.