The practice's design of a canoeist's profile in full motion with jetties opening out onto the Leeds and Liverpool Canal in South Sefton won over the judges.
Once built, the pavilion will provide leisure resources to the local community, as well as being a landmark piece of art in the public realm.
Duggan Morris Architects director Joe Morris said: "We believe our design will complement the regeneration already taking place in the area and will enhance the work already completed. We can't wait to get started and are looking forward to spending a lot of time in the area as we move forward."
Merseyside's housing market renewal public realm manager Paul Kelly added: "We believe we have chosen the design that will offer the most to the area."