We examined spatial and temporal relationships between snow crab Chionocetes opilio, shrimp Pandalus spp., Atlantic cod Gadus morhua and the environment (depth, temperature and salinity) on the Newfoundland-Labrador Shelf from 1995 to 2009 using autumn multispecies trawl survey data. First, the core habitat of snow crab and shrimp was determined based on cumulative distribution functions of species abundance over depth and bottom temperature. On average, this method predicted the presence of crab and shrimp at 95 and 99% of trawl locations, respectively, and indicated 90% of crab and shrimp inhabited temperature ranges of -1 to 4 and 0 to 4°C and depths of 100 to 500 and 150 to 450 m, respectively. Then geographically weighted regressions, based on trawl stations where species presence was predicted, indicated spatial non-stationarity between invertebrates and explanatory variables at scales <200 km. Snow crab abundance was best predicted by environmental variables, suggesting bottom-up influences are important, whereas shrimp abundance was influenced by both the environment and cod (predator) abundance. We discuss how averaged ecological relationships within large marine ecosystems central to fisheries management mask processes operating at smaller scales, with reference to the northern cod ecosystem under present conditions of warming waters and increasing cod.