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Yes, weeds will grow through pea gravel but you can prevent this during the installation process. Install a weed barrier underneath pea gravel and swap it out every three years to keep weeds at bay.

There are organic herbicide options that will kill grass but not flowers, including white vinegar or a dish soap solution. Commercial selective herbicides can also target grass over other plants, but read the instructions carefully to avoid damaging your garden. Herbicides that kill grass but not flowers usually include ingredients like clethodim and sethoxydim. Otherwise, your best bet will be to weed by hand.

Some of the particular herbicides that work best to get rid of nut grass without killing the grass include Halosulfuron-methyl, mesotrione, sulfentrazone, and metsulfuron. A herbicide like glyphosate would kill nutgrass, but it will kill nearby plants, too.

The most effective way to eliminate quack grass without killing the grass nearby is to overseed the area, keep the seed wet until it grows, mow often, and regularly fertilize the area to promote healthy grass that can choke out the invasive weed.