QMs colonize pipes, docks, locks, ship hulls, water intake pipes, other mollusks and cause extensive damage to water treatment facilities.

For Great Lakes water users with lake water intake structures, Park and Hushak (1999) report that total monitoring and control costs were $149 million from 1989 to 1994, and averaged $37 million annually from 1992 to 1994.

According to the Agricultural and Resource Economics Review (April 2006), A number of sources report the general costs of the mussel to be around $6.5 billion for a 10-year period (1990-2000) in the Great Lakes. However, another estimate puts the cost of damages over 10 years to intake pipes, water filtration equipment, and power plants at $3.2 billion.

QMs clog pipes and intake structures causing severe damage that requires heavy annual maintenance

In addition to damaging water systems, QMs disrupt the food chain by consuming nutrients used by other species. Due to massive populations, QMs can consume so much plant life that water begins to clear up. Parks personnel in the Great Lakes region report that water once visible to depths of 6 to 12 inches have been clearing up to astonishing depths of 10 to 12 feet.

Clearer water negatively affects aquatic ecosystems. Many small aquatic animals no longer have sufficient nutrients. For example, the average weight of a Whitefish in the Great Lakes has gone from 5 lbs. in 1988 to 1.6 lbs. in 2006. Also, clearer water allows a deeper penetration of sunlight that can stimulate the growth of bluegreen algae causing taste and odor problems in drinking water. This is cause for specific concern for SLO County reservoirs since both Santa Margarita Lake and Lopez Lake provide drinking water to agencies throughout the county. Some fear that if QMs are not kept out of local reservoirs, water customers will end up paying for additional cleaning and filtration systems.

QMs are filter feeders that absorb heavy metals, trace elements, toxins, and chemical contaminants in their tissues. These absorbents can be passed up the food chain when QMs are eaten by water fowl and other organisms. There have been massive die-offs of water fowl in the Great Lakes region due to Quagga and Zebra Mussels.