Roundup controls thistles but should not be used near water supplies. Natural weed killers such as Burnout can offer control for those that to not want to spray traditional herbicide. Crossbow is available at any large home improvement store and is safe to use closer to water supplies.
Any herbicide that attacks the root system is a good choice for controlling thistles. The time of year the herbicide is applied affects how well it works over time. Biennial thistles are controlled best when herbicides are sprayed before flowering. Perennial thistles should be sprayed when buds are forming in early summer. Preen is a weed preventative that can be safely used for weed control that lasts up to four months and can be used year round. Ortho Groundclear can be used on patios and walkways to eliminate all vegetation.
Do-it-yourself types can mix vinegar and lemon juice in equal parts and apply it to thistles for short term control. Any herbicide must be used as directed for safety and optimum effectiveness. Some people choose to use multiple herbicides at different times of the year for better control. Many chemical herbicides are also available in granulated form for lawns and those that do not own sprayers.