Quantum emitters (QEs) based on deep-level defects in hexagonal boron nitride (hBN) layers are promising alternatives to other qubit-candidates in three-dimensional wide bandgap semiconductors. The two-dimensional (2D) form factor of hBN allows the possibility of near-deterministic placement of quantum emitters and an ease of property-tuning via different means, such as application of strain. However, the 2D nature of hBN also results in a unique set of challenges, including a sensitivity of the QEs to their environment that can influence their different properties, such as their emission frequencies and brightness. In particular, although observed experimentally, theoretical works thus far have ignored substrate-induced modulation of hBN's QE properties. As a result, to date, the magnitude of substrate effects and the underlying mechanism(s) involved in the modulation of QE properties remain unknown. In our density functional theory-based work, we use silicon dioxide as a prototype substrate to demonstrate that the substrate effects can indeed have a significant impact on ground-and excited-state properties of defects responsible for quantum emission. Our analysis shows large structural distortions at the defect sites due to substrate interactions, resulting in significant changes in quantum emission frequencies. These calculations reveal that accounting for substrate effects is critical to the successful use of hBN in quantum sensing and quantum computing.