Legionella, the bacterium that causes Legionnaires’ disease, can grow and spread in building water systems and devices. The COVID-19 pandemic impacted building water systems through reductions in water usage. Legionella growth risk factors can be mitigated through control measures, such as flushing, to address stagnation, as part of a water management program (WMP). A national lodging organization (NLO) provided WMP data, including Legionella environmental testing results for periods before and during the pandemic. The statistical analysis revealed an increased risk of water samples testing positive for Legionella during the pandemic, with the greatest increase in risk observed at the building’s cold-water entry test point. Sample positivity did not vary by season, highlighting the importance of year-round Legionella control activities. The NLO’s flushing requirements may have prevented an increased risk of Legionella growth during the pandemic. However, additional control measures may be needed for some facilities that experience Legionella detections. This analysis provides needed evidence for the use of flushing to mitigate the impacts of building water stagnation, as well as the value of routine Legionella testing for WMP validation. Furthermore, this report reinforces the idea that WMPs remain the optimal tool to reduce the risk of Legionella growth and spread in building water systems.