If problem species show up in a planting, it is much easier to deal with them right away. If unattended, they may spread and completely take over a native reconstruction. Walk your site regularly and cut, pull, or carefully spot spray with Roundup to eliminate these weeds early on. Watch specifically for Canada Thistle, Birds Foot Trefoil, Leafy Spurge, and Sweet Clover. Most annual broadleaf weeds are not a problem as mowing will control them and they will soon be crowded out by the prairie plants.
If problem cool season grasses such as Quackgrass, Brome, or Kentucky Bluegrass begin to invade the site, they can be controlled in one of two ways. A late burn, after these grasses are several inches tall, will stunt them and allow the prairie to out compete them. Cool season grasses can also be controlled with a grass herbicide such as Poast. Herbicides should be applied when the weedy, cool season grasses are three or four inches tall. This will be before your prairie grasses have emerged so they will not be affected. Poast is available at may farm chemical stores. Flowers are not affected in any way by Poast.