Waltl was born in Wasserburg and studied at Landshut and Munich, graduating in medicine in 1819. He then travelled in Austria, France and Spain. In 1833 he became a teacher in Passau, and in 1835 a professor of natural history at the university.
In 1839 he published "Reise durch Tyrol, Oberitalien und Piemont nach dem südlichen Spanien" (Journey through Tyrol, northern Italy and the Piedmont to southern Spain). Also, he was the author of several mineralogical/geognostic works associated with Passau and its environs.