In the US, Xylene and Acrolein were used to control irrigation weeds until the past 20 years, when the two formulations of endothall were labeled for irrigation use as Cascade and Teton. In addition to continued use of Acrolein in some districts, complexed copper products are used to control algae and some weeds. For the most part, these are the only herbicides used to control submersed weeds in irrigation canals. Generally, these herbicides are metered in to maintain a desired concentration for a specific amount of time.
Mechanical techniques include chaining, excavation (particularly at any grates or gates), and a very limited amount of mechanical harvesting. The most common is chaining, in which a heavy chain is dragged along the bottom to uproot weeds and allow them to drift down to collection points.
The main physical control is the use of dewatering and exposure, which controls some species but does not impede many species that are adapted to this hydrological pattern.
Beginning in the 1950's, scientists from USDA Agricultural Research Service, Bureau of Land Management, and the US Army Corps of Engineers studied methods to manage weeds in irrigation canals. As time passed, agencies dropped their interest in the management of weeds in irrigation systems. Scientists at several land grant universities in the past have also provided third-party research on managing weeds in irrigation systems. At this point, essentially all of the research on weed management in irrigation systems is accomplished by the companies that develop and market herbicides.
Photos: Top,CA; bottom, Removing seeds from irrigation canal near Tulare, CA using chaining.

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Source : ucanr.edu