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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.

Adding vinegar to your lawn increases the acidity of the area, which can kill quack grass present above the ground. However, putting vinegar in your yard will also kill the grass. Unfortunately, the below-ground quack grass rhizomes remain very much alive in the presence of vinegar and will soon sprout again.

Several tools exist that can help remove unwanted grass. The one you choose depends greatly on how much you need to remove and how hard you'd like to work. A sod or turf cutter is the fastest method while using a shovel is labor-intensive and much slower. You may also need a garden rake, tiller, and wheelbarrow. 

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.