Born in Madrid in 1941. He dropped out of the Engineering and Telecommunications School to attend the Royal Conservatory of Music in Madrid, where he studied piano, harmonics, counterpoint and composition. In 1968, he received a diploma in teaching composition.

Between 1966 and 1970, he studied instrumentation with Günther Becker during the Darmstadt Summer Courses. In 1969, he earned a scholarship from the Juan March Foundation to train at the Psychoacoustics and Electronic Music Institute at the University of Ghent. The following year, one of his first electroacoustic works (Rabelaisiennes, for prepared guitar, magnetic tape, and filters) was nominated for the Gaudeamus Festival Award.

He was a member of the Koan group, as both compositor and musician, during its early period (1967-1970). In 1969, he started working with the Alea laboratory in Madrid. Between 1970 and 1972, he was part of the Alea Música Electrónica Libre group, the first Spanish group playing live electroacoustic music.

In 1976, he moved to Barcelona where he worked closely with the Phonos Laboratory.

In 1983, he founded Obert-Art Actual, together with Rafael Santamaria, organising the annual multimedia festivals Sis Dies d'Art Actual in Barcelona from 1983 to 1985. He then started Multimúsica in 1985, with Gabriel Brncic and Claudio Zulian, a group specializing in live electroacoustic music.

One of the characteristics of his work since 1969 is the almost total absence of traditional instruments in favour of electroacoustic sources. Eduardo generally interprets his own work in concerts, combining magnetic tapes, synthesizers and processors in real time — often accompanied by videos or other elements created by visual artists.

Among the most imposing examples of this cooperation with these plasticians are: “Calidoscopi” (1976), an audiovisual spectacle with lights sculptures by Eduardo Magliano, Sala Zeleste, Barcelona ; “ Per a Matar·ho ” (1977), a performance with the painter Ferran García Sevilla, Mataró, Barcelona ; “Dempeus Assegut Agenollat” (1981), an action with Rafael Santamaria, Espai 10 - Foundation Miró, Barcelona ; “Sottovoce” (1983), musical environment for a video installation by Rafael Santamaria, Metrònom Gallery, Barcelona ; “Vilafranca-Eclipsi” (1985), video installation with Carles Pujol, Sant Joan’s Chapel, Vilafranca del Penedès, Barcelona ; “El Lloguer del Miraller” (1987), performance with Rafael Santamaria, Tramesa d'Art en favor de la creatividad, Palau de la Música, Valencia ; “Alteraciones” (1989), a spectacle with sound sculptures and lights with the painter Toni Rueda, Encontre de Compositors X, Palau Solleric, Palma de Majorca ; “Electroacústica, Visuales y Grand Chapeau Chinois” (1991), performance with photography by Santiago Torralba, 4 Minimalismos 4, Autumn Festival of the Madrid Community ; “Tócame una poloniesa” (1993), Foundation Antoni Tàpies, Barcelona and “Ressó, Imatges • Performance Electroacústica” (1994), Foundation Pilar y Joan Miró, Palma de Majorca, concerts with slides by Santiago Torralba and videos by Carles Pujol ; “Música imaginada” (1996), spectacle with films and slides by Santiago Torralba and Pablo Arribe, Reina Sofía Museum, Madrid ; “L'Arc” (1997), installation with Carles Pujol, Caixa de Manresa, Manresa, Barcelona; "Einai"(1998), video with Eugeni Bonet; "Sugar Cane" (2000), Installation with Xabela Vargas, Huelva Museum. Voz (2001), film by Javier Aguirre; El sueño de Akshoo (2004), video by Ana de Alvear; Dispersión de la luz (2005), film by Javier Aguirre; Glosa a Acariño (2007) soundtrack for a fragment of the film "Acariño galáctico" by José Val del Omar; Etoile de mer (2009), soundtrack for a film by Man Ray; Brief Fast Ambrosia (2010), video by Carlos Urbina; Beyond us (2010), show with multi-channel video by Ana de Alvear and electroacoustic octophonic device; 1 + 1 = 1 (2011), video show by Santiago Torralba and electroacoustic octophonic device; George's Odissey (2014), MNCARS, Madrid; Un día como hoy (2023), video by  Ana de Alvear.

He is the author of three electroacoustic operas: Uno es el Cubo · fantasía kepleriana en cinco sólidos perfectos, Dulce mal and Ritmos de vidrio roto, all premiered in the International Festival of Contemporary Music of Alicante (1995, 1999, and 2010, respectively).

Eduardo co-founded the Electroacoustic Music Association of Spain and was its President between 1988 and 1994; he was in charge of the first and second editions of the Punto de Encuentro International Festival (1990 and 1992). He has been a member of the International Academy of Electroacoustic Music of Bourges and of the Area of Acoustic Creation Foundation of Mallorca.

In 1994, he was awarded the Magisterium of the Grand Prix International de Musique Électroacoustique in Bourges (France).

In 1996 he moved to Huelva, where he founded Musical Creation and New Technologies and the Diáfano electroacoustic music studio. In 2000, backed by the Regional Government of Andalusia, he created the Confluences, art and technology at the edge of the millennium cycle, which he directed until its disappearance in 2006. In 2003 he created the International Competition of Electroacoustic Miniatures, which has been held seven times under the sponsorship of the Regional Government of Andalusia. In 2006, he created — and directed, until 2008 — the International Congress of Music and Contemporary Technologies of the University of Seville.

Recordings of his works are published among more than 50 record publications. La mà de Guido, on his Ars Harmonica label, has published his Anthology, 1969-2014 Edition on two DVD’s that include 48 works covering a period of 45 years, as well as the DVD “1 + 1 = 1 Música imaginada” (with the support of the SGAE Foundation), which includes 5 of his works in collaboration with artist Santiago Torralba. María de Avear World Edition has published the book “Eduardo Polonio – From Serialism to Multimedia” (2021), accompanied by a CD with his most recent works (2015-2021). In April 2023, Polonio published his latest book “Las matemáticas, la música y el músico (yo)” in Edict Oràlia.