Despite sporadic observations of the vase tunicate, Ciona intestinalis, on boats and mooring structures in Charlottetown Harbour, Prince Edward Island, the species has not established a population in the harbour nor dispersed the ~12 km downstream to Hillsborough Bay, an important source of blue mussel (Mytilus edulis) spat for the PEI aquaculture industry. A population matrix model used in conjunction with an oceanographic model suggests that advection of larvae from the harbour to the spat production area requires more than one or two generations, and the use of intermediate settlement nodes, such as navigational aids and aquaculture sites located in the upper part of Hillsborough Bay, as ‘stepping stones’. Maintaining potential settlement nodes in a tunicate-free condition could delay oceanographic dispersal of C. intestinalis within the estuary. According to observations of colonial tunicate dispersal in 2010, most likely originating from colonies established in the same locations where C. intestinalis inoculations have been detected, dispersal was occurring in the vicinity of one of the nodes identified by the model as priorities to be monitored for early detection of tunicate settlement, but had not yet reached the other node. A major finding is that the dispersal of solitary tunicates by oceanographic processes, often considered uncontrollable, is evidently amenable to management through monitoring and cleaning of the intermediate settlement nodes.