Born in Middelburg, Holland, he studied medicine at the University of Caen, graduating in 1618. In the following years he taught at various colleges, before taking on, in 1627, the job of Rector at Dordrecht, which, under his leadership, became Holland's most prestigious school. In the college grounds, Beekman set up, in 1628, the first European meteorological station, undertaking an accurate data sample of precipitation, temperature variation, wind speed and direction, and compiling numerous astronomical observations. After meeting Descartes, in Breda in 1618, he befriended him, initiating a relationship which, despite its instabilities, was extremely fruitful on the intellectual level, and remains of great interest both for the history of philosophy and the history of science.
A Copernican in cosmology, Beeckman shared Harvey's ideas on the circulation of the blood, and developed a perspective in physics with atomistic tendencies. From 1613, his studies on dynamics lead him to recognise the principle of inertia and of identical velocities for falling bodies in a vacuum. He was an active experimenter, developing elaborate empirical solutions to study various problems in physics. In 1626, he determined the relation between pressure and volume in a given quantity of air, discovering that pressure grows at a slightly faster rate than the lessening of volume. In his studies on pneumatics, Beekman refused the explanation of the rise of water in the pump based on the theory of the horror vacui, recognising that it was air-pressure which caused this phenomenon.

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