After a course of scientific studies in his native city he travelled throughout Asia Minor collecting data on the Ottoman Empire's military organisation, as well as on its natural history.

On his return he entered the service of the Emperor Leopold (1682) and fought with distinction against the Turks, by whom he was wounded and captured in an action on the River Rába; sold to a pasha who met him after the Battle of Vienna, his release was secured in 1684.

Count d'Arco was beheaded because he was found guilty of capitulating before necessary, while Marsigli was stripped of his titles and honours by the Holy Roman Emperor, and his chivalric sword was broken over him.

After he had left the Habsburg Army he made journeys to Switzerland and then France, spending a considerable time at Marseilles undertaking studies about the nature of the sea.

He drew plans, made astronomical observations, measured the speed and size of rivers, studied the products, the mines, the birds, fishes, and fossils of every land he visited, and also collected specimens of every kind, instruments, models, antiquities, etc.

His principal works are the following: Osservazioni interne al Bosforo Tracio (Rome, 1681); Histoire physique de la mer, translated by Leclerc (Amsterdam, 1725); Danubius Pannonico-Mysicus, richly illustrated work in six volumes containing much valuable historic and scientific information on the river Danubius, (6 vols., The Hague, 1726); and L'Etat militaire de l'empire ottoman (Amsterdam, 1732).