Zehnder was born on 21 February 1946 in Goldach.[1] He studied natural sciences at ETH Zurich where he graduated in 1971. Zehnder subsequently moved to Rabat, Morocco, where he worked as a consultant for the World Health Organization until 1973.[1] Back in Switzerland Zehnder obtained his PhD in microbiology from ETH Zurich in 1976.[1][2] During his PhD work Zehnder managed to discover and isolate Methanothrix soehngenii, which fellow microbiologist Willem Meindert de Vos described as a major discovery.[3] He subsequently spent two years in the United States as a research associate in the bacteriology department at the University of Wisconsin–Madison.[1][2] Zehnder then moved to Stanford University where he was employed as assistant professor in the department of civil engineering.[1]
In 1982 Zehnder was appointed professor of microbiology at Wageningen University & Research in the Netherlands. He also became head of the Institute of Microbiology.[1] During his period the research at the university became more focused on anaerobic and environmental microbiology. There was studies performed on microbial phosphate removal and biofilm formation.[3] In 1992 he became both director of the Swiss Federal Institute of Aquatic Science and Technology and professor of environmental biotechnology at ETH Zurich. He held positions until 2004.[2] In May 2008 Zehnder formally retired.[1] From July 2004 until December 2008 he was president of the ETH Board.[1] During this period he aimed to bolster the international reputation of the institution.[4] He received critical reviews, being described as "a nice person in the wrong place".[5] From 2008 until 2010 he also served as scientific director of the Alberta Water Research Institute.[1][2][6] From 2011 he served as visiting professor to Nanyang Technological University in Singapore.[6]
Zehnder's fields of expertise include water, in both qualitative and quantitative aspects and the relation between water and food security.[7] Water shortages in relation to climate change has been a main topic for him.[8] During his career he published more than 250 papers and supervised more than 80 PhD students.[2]