Biological hotspots are places with outstanding biodiversity features, and their delineation is essential to the design of marine protected area networks (MPANs). For the Central Coast of Canada’s Northern Shelf Bioregion, where a MPAN is being developed, we identified hotspots for structural corals and large-bodied sponges, which are foundation species vulnerable to bottom contact fisheries, and for Sebastidae, a fish family that includes long-lived (> 100 years) and overexploited species with high trophic positions. Using 10 years of survey data that spanned from inland fjords to oceanic waters, we derived hotspot indices that accounted for species characteristics and abundances, and examined hotspot distributions across depths and oceanographic subregions. The results highlighted previously undocumented hotspot locations for each species group, thereby informing the placement of MPAs for which high levels of protection are warranted. Given the vulnerability of the species groups that we examined to cumulative fishery impacts, prospective MPAs derived from our data should be considered for interim protection measures during the protracted period between final network design and the enactment of MPA legislations. These recommendations reflect our scientific data, which are only one way of understanding the seascape. Our extensive surveys did not cover many locations known to Indigenous peoples as biologically important. Consequently, it is paramount that Indigenous knowledge also contributes substantially to the design of the MPAN.