The application of molecular beacons (MB) that bind to precise sequences of mRNA provides a near-universal approach in detecting evidence of viral replication. Here, we demonstrate the detection of BK Polyomavirus (BKPyV), an emerging indicator of microbiological water quality, by a quantum dot-based MB. The MB allowed us to rapidly characterize the inactivation rate of BKPyV following exposure to a solar simulator (kobs = 0.578 ± 0.024 h(-1), R(2) = 0.92). Results were validated through a traditional cell-culture assay with immunofluorescence detection (kobs = 0.568 ± 0.011 h(-1), R(2) = 0.97), which exhibited a strong correlation to MB data (R(2) = 0.93). Obtaining solar inactivation rates for BKPyV demonstrates the first use of a MB in characterizing a microbiological inactivation profile and helps assess the appropriateness of adopting BKPyV as an indicator organism for water quality.