You'll want to pay attention to this kayaking recommendation because this is the only kayaking company based on the Nova Scotia side of the Bay of Fundy.
Nova Shores Adventures operates out of the beautiful village of Advocate Harbour, with tours focusing on the coast surrounding Cape Chignecto Provincial Park. There are definitely some secluded beaches, rock formations, cliff arches and coves that you can only explore in this part of Fundy by kayak. Nova Shores does half-day, day and multi-day tours.
Owners Else Marie and Werner have a vast amount of experience offering kayak tours. Nova Shores orginally offered excursions along the coast near Peggy's Cove (outside Halifax - about 2.5 hrs from Fundy!) but when Else Marie and Werner started personally kayaking this part of the Fundy coast they liked it so much that they packed up and moved there!
(BTW tours are still offered by their great staff at the Dover location for Peggy's Cove area).