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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.

Yellow leaves and stems on your sprouts indicate they’re not getting enough light. Keep them near the appropriate light source and give them as much as they need (they require longer exposure to fluorescence than they do to natural light sources).

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.

Glyphosate and other non-selective herbicides can kill orchard grass, but they will also kill the surrounding plants. Also, not all areas allow the use of glyphosate due to its environmental impact—which the EPA describes as a "potential risk to terrestrial and aquatic plants and birds, and low toxicity to honeybees." Consider mechanical removal to target the plants specifically.