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Weeds can grow through rubber mulch, but it depends on if you removed all the weeds in your garden beforehand. Weeds already in the soil can grow even when using rubber mulch. However, that doesn’t mean that your garden will be littered with rubber and weeds, but it does mean that the occasional weed might still pop up. Another way you can increase your weed suppression is by using landscape fabric as a second layer. 

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.

Crabgrass is very resilient, and homemade solutions like vinegar may not be strong enough. Typically, hand-weeding is the most effective option that doesn’t involve harmful chemicals. You can use corn-meal gluten as a natural pre-emergent herbicide, but it’s not as effective as chemical weed killers.

You should add 1 to 4 inches of mulch, depending on your garden type and needs. Keep in mind that no amount of mulch can completely prevent weeds, but a heavier coverage (closer to 4 inches) can suppress weeds enough that you are only seeing them sprout every few weeks. Finer mulch prevents weeds more effectively than large mulch, so if you’re using mulched leaves or shredded bark, 1 to 2 inches will likely suffice, while 3 to 4 inches is best for larger mulch, like bark chips or straw.