The US Northeast Continental Shelf is experiencing a period of increasing temperature levels and range, which impacts the quantity of thermal habitats within the ecosystem. With increasing temperatures, the amount of warmer, surface water thermal habitats (16–27 °C) has increased while there has been a reciprocal decline in cooler water habitats (5–15 °C). These cooler water habitats are the most abundant and comprise the core habitats of the ecosystem. The coldest thermal habitats (1–4 °C), however, have increased slightly in amount or have remained constant, reflecting a discontinuity in the progression of warming along a latitudinal gradient. This discontinuity may be the result of recent changes in the circulation of water masses in the northern Gulf of Maine, potentially associated with the Labrador Current. The contraction of core thermal habitats appears to have had biological consequences on multiple trophic levels. In particular, two zooplankton species associated with the larval feeding of Atlantic cod, Gadus morhua, have declined in abundance in the same areas where cod populations have exhibited continually poor recruitment. The zooplankton species group Pseudocalanus spp., which is associated with winter-spawning cod, has declined on Georges Bank and in the Eastern Gulf of Maine. The zooplankton Centropages typicus has declined in the Gulf of Maine during late summer into fall, potentially affecting spring-spawning cod in that area. These observations are consistent with the hypothesis that portions of the population complex of cod have lower reproductive output due to changes in zooplankton abundance, which we associate with the distribution of temperatures within the ecosystem.