Prechlorination is the most common strategy for zebra and quagga mussel control in drinking water treatment plant intakes in the Great Lakes region. Although effective and inexpensive, chlorine can form regulated disinfection byproducts. Two potential alternatives to prechlorination were evaluated for mussel control: peracetic acid (PAA) and EarthTec QZ, a copper-based product. Pilot-scale experiments were conducted to test EarthTec QZ for veliger control and to evaluate the efficiency of PAA and EarthTec QZ for adult mussel control. EarthTec QZ doses of 30, 60, and 120 μg/L as copper ions demonstrated dose-dependent veliger control at 12 °C. PAA doses of 5, 10, and 25 mg/L were effective for adult mussel control at the low water temperatures tested (4 °C). Results from this study indicate that PAA and EarthTec QZ may be an alternative to prechlorination.