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First choice: Thistle Inn . Happy hour with half price drinks and (I think) 2 half priced appetizers in the pub from 5:00 to 6;00PM. Not on the water, but they have nice patio dining for dinner:
http://www.thethistleinn.com/Also good:
Boothbay Harbor
http://www.mcseagullsonline.com
http://www.theboathousebistro.com/East Boothbay
http://www.lobstermanswharf.comI'll be there soon. Please post what you liked (or not).
Cheers...
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Thistle Inn
55 Oak St, Boothbay Harbor, ME 04538