Here's some sites on milfoil - one example of state's control strategies, and another state's prevention program

http://www.ecy.wa.gov/programs/wq/plants/management/DrawdownStrategies.html

http://www.mainevolunteerlakemonitors.org/mciap/herbarium/VariableWaterMilfoil.php

"Prevention and Control

The best way to control this species or any aquatic invader is to prevent it from being introduced in the first place. Anyone engaged in activities in Maine’s waters should be aware of the potential for spread of invasive plants and take steps to prevent their introduction. Your actions can make a difference. Simple things you can do include inspecting boats, motors, and trailers at the boat ramp before launching and again after hauling them out. Prevent plant material from getting into bait buckets and live wells, and from getting tangled up in anchor ropes or fishing gear. Plants cleaned from boats and gear should be disposed of in a trash receptacle or away from water on dry land.

Once established, invasive aquatic plants are extremely difficult to eradicate."