Margenau worked on the theory of microwaves and the development of duplexing systems that enabled a single radar antenna both to transmit and receive signals.

"Our thesis is that quantum mechanics leaves our body, our brain, at any moment in a state with numerous (because of its complexity we might say innumerable) possible futures, each with a predetermined probability.

"[4] Margenau served on a commission of the World Council of Churches in developing an ecumenical position on nuclear weapons and atomic warfare.

However, his book The Miracle of Existence (Ox Bow Press, 1984) shows Margenau's broad interests not only in Christianity, but also in Eastern religions and his fascination with finding connections among different religious and philosophical traditions.

Margenau was appointed Eugene Higgins Professor of Physics and Natural Philosophy as Yale in 1950, a post he was to hold until his retirement from formal academic life in 1986.