The transition from noisy intermediate-scale quantum (NISQ) processors to large-scale fault-tolerant machines requires more than incremental improvements in physical qubit fidelity. While advances in quantum error correction (QEC) theory continue to lower the theoretical overhead of quantum computing, much of this research remains abstracted from the physical realities of qubit implementations. This disconnect often results in hardware-agnostic designs that are inefficient or impractical to build. In this dissertation, I identify three primary gaps between theoretical QEC research and practical hardware: (1) the high levels of noise and temporal instability in experimental devices that impede scalable QEC; (2) the prohibitively large qubit and time costs of useful algorithms, driven largely by the limitations of the standard surface code; and (3) the failure of current resource estimates to account for hardware-level constraints, such as limited connectivity and the complexity of implementing non-local operations. To bridge these gaps, I propose a holistic, cross-stack approach where the error correction protocols and the physical hardware are designed in concert. By developing realistic device models and hardware-aware solutions at the lowest levels of the software stack, we can accelerate the path toward functional fault-tolerance. I present my work across three research thrusts: first, leveraging codesign to mitigate hardware-specific noise and reduce physical error rates; second, developing software tools for fault-tolerant quantum computers to reduce the space-time overhead of the QEC layer; and third, proposing two novel hardware-aware QEC architectures that provide practical, high-performance routes to scalable quantum computation.
