One of the prevailing arguments of the day that Pettenkofer focused on was the relationship between sewage and the health of a population. In one of his first major projects in his home city of Munich Pettenkofer advocated for the development of running water throughout the city. He also emphasized the selection of the Mangfall River, not the readily at hand and highly polluted Isar River, as the source of the city's drinking water. Many of his additions and plans for the city's sewage system are reflected today in the current sewage system layout.