Atlantic cod ( Gadus morhua ) distribution patterns and the behavioral (site fidelity), biotic (prey and predators), and environmental factors that determine them are fundamental to cod’s historic importance as a commercial species in the North Atlantic. Using classification and regression tree analysis (CART), we compared two periods (1991–1995 and 1998–2004) with contrasting bottom temperature and salinity regimes to determine regional factors that best explained cod distribution and catch weight per tow from summer surveys in the northern Gulf of St. Lawrence (the feeding period of cod). The classification tree analysis indicated that the presence or absence of cod was chiefly determined by depth in both of these periods. In contrast, the regression tree analysis determined that cod catch weight distributions were explained by different variables in each period. In the colder period (1991–1995), the distribution of catch weights was explained well by environmental variables (bottom temperature, salinity, depth); however, in the warmer period (1998–2004), distributions were best explained by variables from the previous year. These results indicate that the spatiotemporal dynamics of environmental conditions are likely to influence the loyalty of cod to specific feeding grounds and imply that cod responses to the environment could be susceptible to long-term environmental (e.g., bottom–habitat) and climate change.