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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.

Mowing a lawn will, unfortunately, not get rid of clover, and it may even encourage it to flourish. Let your lawn grow to a healthy height of over 3 inches and then set your mower blades no lower than this level. Higher grass will cut out the light that clover loves and discourage it from spreading.

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. 

Very carefully. You should be cautious when using any of the above methods, as any one of them could lead to you accidentally killing desired grasses and plants. However, there are selective herbicides that can target certain plants over others. Look for a product that only affects the type of weeds you want to eliminate and spares the plants you want to keep.