Often, there are crystals in your dog's urine instead of stones. These crystals might be a warning sign of stone risk. It depends on the type of crystals, dog breed, and presence of a UTI. Couch grass-root contains disinfecting and anti-inflammatory properties that may help eliminate urine crystals in dogs when they're at an early stage. Adding glucosamine to your pet's diet can prevent irritation from crystals in a dog's urine.