Quantum simulation offers a powerful approach to studying quantum field theories, particularly (2+1)D quantum electrodynamics (QED$_3$), which hosts a rich landscape of physical phenomena. A key challenge in lattice formulations is the proper realization of topological phases and the Chern-Simons terms, where fermion discretization plays a crucial role. In this work, we analyze staggered and Wilson fermions coupled to $\text{U}(1)$ background gauge fields in the Hamiltonian formulation and demonstrate that staggered fermions fail to induce (2+1)D topological phases, while Wilson fermions admit a variety of topological phases including Chern insulator and quantum spin Hall phases. We additionally uncover a rich phase diagram for the two-flavor Wilson fermion model in the presence of a chemical potential. Our findings resolve existing ambiguities in Hamiltonian formulations and provide a theoretical foundation for future quantum simulations of gauge theories with topological phases. We further outline connections to experimental platforms, offering guidance for implementations on near-term quantum computing architectures.
Comment: 25 pages, 12 figures