Brown the kielbasa rounds in a skillet over medium-high heat until their cut sides color, 5 to 6 minutes.
Add the kielbasa, navy beans, kidney beans and onion to a 5- or 6-quart slow cooker.
Whisk the ketchup, maple syrup, molasses, vinegar, mustard, Worcestershire, paprika and pepper until smooth.
Pour the sauce over the beans and fold gently until everything is coated.
Cover and cook on low for 5 to 6 hours until the onion is tender and the sauce is dark and thick.
Uncover and cook on high for 15 minutes if the sauce still runs quickly from a spoon, then stir before serving.