Born in Warsaw, Kotoński studied there with Piotr Rytel and Tadeusz Szeligowski at the PWSM, graduating in 1951.
In an initial period of activity he took an interest in folk music from the Podhale region in southern Poland.
He also worked in various electronic music studios abroad, amongst others in Cologne, Paris, Freiburg, and Berlin.
He presented guest lectures in composition and electroacoustic music at foreign universities in, amongst others, Stockholm, Buffalo, Los Angeles, and Jerusalem.
His students included: Jacek Grudzien, Jarosław Kapuściński, Krzysztof Knittel, Konstancja Kochaniec, Stanislaw Krupowicz, Owen Leech, Hanna Kulenty, Pawel Mykietyn, Pawel Szymanski.