The coastlines in this ecozone vary considerably. Precipitous fjords and cliffs are common around the coasts associated with Baffin Basin, Lancaster Sound and Nares Strait whereas areas to the west like the Foxe Basin, Amundsen Gulf and Viscount Melville Sound have flat to rolling coastal plains. Water depths of 150 to 500 metres are typical. Deeper water starts to occur when this ecozone merges with the Northwest Atlantic Ecozone; around Baffin Bay, depths can start to approach 1000 metres. Massive glaciers along Baffin and Ellesmere islands often reach from the mountain tops and into the sea. On eastern Ellsemere Island, glaciers extending into the sea break off or "calve" huge icebergs into Nares Strait.

During the winter, sea ice is jammed fast to the land and extends over the seas as a solid sheet. Polynyas, localized breaches in the ice where currents and upwellings create open water, can occur throughout the ecozone. The ice cover reaches its maximum thickness in May. In the brief spring and summer periods, the ice will breakup. In the northwestern parts of the ecozone, the sea ice normally shatters into massive sheets that are separated by narrow channels of open water. The sea ice persists throughout the summer. In the rest of the ecozone, the ice is more seasonal. In summer, the massive sheets of ice fracture, drift and melt away. The process can be very dramatic. Shorelines can be markedly scoured by drifting fragments of ice or huge log-jams of ice can be driven up on the beaches. As the summer periods proceeds, open water can be found further and further north. From year to year, ice conditions are so variable and unpredictable, however, that mariners and navigators of even the most technologically advanced ships can still find themselves blocked. By September, most of the sea ice in the south easterly parts has either melted or drifted away on southerly currents.

The short cool summers of the Land of the Midnight Sun give way to long cold winters. Long periods of daylight in the summer help stretch the short growing season, but air temperatures remain stubbornly chilly. Even in July, mean daily temperatures average just 10°C. In winter, temperatures average about -30°C, and often much lower. In the southern range of the ecozone lie Hudson and James bays, where the waters are amongst the shallowest (50 to 150 metres) and the climates are the most temperate.