Ekman was a member of a consortium of Scandinavian scientists who transformed the study of oceanography and meteorology at the turn of the twentieth century. Ekman's father, Fredrik Laurentz Ekman, was an oceanographer, but Vagn Ekman's greatest influence came from Vilhelm Bjerknes, whose work in hydrodynamics and atmospheric movements inspired Ekman to ponder similar movements in the circulation of the oceans.

Ekman's colleague Fridtjof Nansen observed how drift ice veered to the right of winds in the Northern Hemisphere and suggested that Ekman study the phenomenon. Ekman eventually developed the theory of the Ekman layer. This layer is the uppermost part of the ocean and is the part that is most influenced by the Coriolis Force. Hence, the same effect that causes circulation in the atmosphere is also at work in the oceans.

In 1923 Ekman created a mathematical model that demonstrated a complete ocean current system for an ocean basin. During the late 1920s, he invented a mechanical current meter that measured the velocity and direction of ocean currents. This device continues to be in use today.

Ekman held various positions as a laboratory assistant at the International Oceanographic Laboratory in Oslo, Norway, and as lecturer and professor at the University of Lund. He published over 100 articles on oceanography and related topics.

Ekman was noted for his honesty and meticulous attention to detail. These traits may be related to his devotion to the Lutheran church, which held absolute truth as its doctrinal focal point.