Put on gloves and pull up the weeds. This is the simplest way to remove a few weeds.
Dig the weeds up with a shovel or spade if the roots are deep. When pulling the weed, if it breaks off without the roots, dig it out. Set the stones aside and dig until the roots are extracted.
Spray glyphosate weedkiller onto the weeds and wait seven days. Follow the label instructions for dosage details. A second application may be necessary to kill the weeds. Pull the vegetation up after it is dead.
Pour boiling water on the weeds. If the weeds are concentrated in a certain area of the stone yard, the heat from the water will kill the weeds.
Spray regular white vinegar on young weeds. Vinegar typically isn't powerful enough to kill established weeds.
Fill a spray bottle with salt water and spray areas that are weed free as a preventative. Salt water kills vegetation, so use it only if you are not planning on growing plants in the area for many months. The salt will take months to completely leave the soil. Until then it will be hard for plants to grow.