Two-dimensional (2D) materials are strongly affected by the dielectric environment including substrates, making it an important factor in designing materials for quantum and electronic technologies. Yet, first-principles evaluation of charged defect energetics in 2D materials typically do not include substrates due to the high computational cost. We present a general continuum model approach to incorporate substrate effects directly in density-functional theory calculations of charged defects in the 2D material alone. We show that this technique accurately predicts charge defect energies compared to much more expensive explicit substrate calculations, but with the computational expediency of calculating defects in free-standing 2D materials. Using this technique, we rapidly predict the substantial modification of charge transition levels of two defects in MoS$_2$ and ten defects promising for quantum technologies in hBN, due to SiO$_2$ and diamond substrates. This establishes a foundation for high-throughput computational screening of new quantum defects in 2D materials that critically accounts for substrate effects.
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