Heat water, red wine, cider vinegar, lemon, 1/2 onion, garlic, cloves, bay leaves, white sugar, salt, juniper berries, and peppercorns in a saucepan over medium heat until sugar is dissolved, about 5 minutes. Allow marinade to cool and pour into a resealable plastic bag. Add beef roast, coat with marinade, squeeze out excess air, and seal bag. Marinate in the refrigerator 2 to 3 days, turning the roast twice a day.
Place onions, carrots, and celery in a slow cooker. Remove roast from marinade and place atop vegetables. Strain marinade and pour 2 1/2 cups over roast; reserve remaining marinade.
Cover and cook roast on Low for 8 hours. Turn slow cooker off. Transfer roast to a cutting board and cover with aluminum foil. Strain cooking liquid into a large bowl and return vegetables to slow cooker to rest.
Heat about 3 cups cooking liquid and gingersnaps in a saucepan over medium-high heat, adding reserved marinade as needed, until gravy is thickened, about 10 minutes.