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Thanks. I've been trying to find a good tool for adding the canonical link to Joomla ... right now I'm using MetaGenerator but it doesn't let me specify exactly what URL should be the canonical and I guess it's just pulling the article and giving it the category alias. Any better idea on how to handle this in Joomla?

No because im guessing each page has a title tag specific to the location, if you merge 2 pages together your end up with one title tag rather then 2. Persoanlly myself I would have a page which lists all the locations called locations.php then link to each city from that page, if you build a few links to the city page your might find the city pages get crawled more often. So your have: vipfishingcharters.com/locations/boca-raton-fishing-charters/