Up until 1904 Brunnthaler was an employee of the Viennese banking and exchange establishment (Voelcker & Co.) — as a botanist he was self-taught. From 1895 he served as librarian of the Zoologisch-Botanischen Gesellschaft (Zoological-Botanical Society in Vienna), and in 1897 he founded the Kryptogamen-Tauschanstalt (Cryptogamic exchange institution). In 1905 at Schönbrunn, he organized a botanical exhibition that was associated with the International Congress of Botanists. In 1908 he was named as a curator of the botanical institute at the University of Vienna.
In 1909 he embarked on a scientific expedition to German East Africa, Cape Colony and Natal, from which he collected valuable specimens. In 1911 he participated on a journey to Dalmatia. During the following year he succumbed to illness and died two years later at the age of 42.
- Die Algen und Schizophyceen der altwässer der Donau bei Wien, 1908 – Algae and Schizophyceae at the oxbow of the Danube near Vienna.
- Vegetationsbilder aus Südafrika (Karroo und Dornbusch), 1911 (in: Karsten and Schenck's Vegetationsbilder) – Botanical images from South Africa: Karoo and Dornbusch.
- Ergebnisse einer botanischen Forschungsreise nach Deutsch-Ostafrika und Südafrika (Kapland, Natal und Rhodesien), 1912 – Results of a botanical research trip to German East Africa and South Africa (Cape Colony, Natal and Rhodesia).
- Vegetationsbilder aus Deutsch-Ostafrika: Regenwald von Usambara, 1914 (in: Karsten and Schenck's Vegetationsbilder) – Botanical images of German East Africa: Rainforest of Usambara.
- Chlorophyceae II: Tetrasporales, Protococcales, Einzellige Gattungen unsicherer Stellung, 1915 (with Ernst Lemmermann and Adolf Pascher) – About Chlorophyceae.
- Literature Archive of the Austrian National Library (July 2009) (biographical information).
- Etymological Dictionary of Succulent Plant Names by Urs Eggli, Leonard E. Newton
- Google Books (list of publications)
- IPNI. Brunnth.