Management techniques used throughout the MLS are site specific and take a landscape scale approach. The Management Plan for the MLS describes recommended methods of control, outlines a management schedule and associated costs, and specifies long-term management strategies for each of seven Phragmites Management Areas. Contingency plans are included in the recommendations, allowing quick adjustments to control activities when site conditions change, without having to go back and seek partner approval. The Management Plan follows the Ontario Ministry of Natural Resources Best Management Practices, which helps build confidence in the approaches. For large sites, a contractor specializing in restoring sensitive habitats, and a burn specialist were hired.
Typically, large, dense monoculture stands are first sprayed with herbicide in August or September, usually from a retrofitted track vehicle, and then are rolled and burned in the next dormant season, from November to March. This timeline reduces negative impacts to native plants, reptiles and amphibians, avoids disturbing birds during critical nesting and fledging seasons (typically April-July), and reduces conflicts with the tourist season. Follow-up treatments are conducted as needed after the initial year of spraying. Lower-density areas are controlled with backpack crews. Volunteers, including some certified technicians, assist with backpack spraying and hand wicking on smaller cells and where follow-up treatments are required. Property owners also help by cutting seed heads or spading (or see Wymbolwood: Management). An airboat is used to control non-native Phragmites along the boat channels and to access islands because this type of boat reduces potential harm to mussels and turtles, which could be hit by prop motors.
Prior to using herbicide for management, manual methods of removal were used and found to be both unsuccessful and labour intensive. After the first year of herbicide treatment, most sites have had 85-95% reductions in non-native Phragmites cover and significant returns of native vegetation.
In Canada, non-native Phragmites in standing water cannot be controlled using herbicide due to the lack of a legally available products, so these areas are cut or rolled to stress the plants and dampen further establishment, spread, and seed head development. However, high lake levels in 2013 and 2014 hampered efforts to restore large sections of Lake Huron meadow marsh, and during the 2014-2015 winter, large iced-over Lake Huron sites were unable to be rolled or burned due to greater than usual snow depths and unsuitable burn conditions. The lack of available herbicides for managing non-native Phragmites in standing water means that some stands that should be high priorities are not managed.