The Environment Ministry of the state of Hesse announced that the deadly O 104:H 4 strain of the bacteria had been found in the Erlenbach stream in the north-east of the city.
A more harmless E. coli strain had been found in a vegetable farm close by the stream last week, when lettuce was apparently contaminated by water used for washing. Following routine checks, the more dangerous E. coli form was then found in the stream.
Susanne Andriessens, spokeswoman for the Hesse health department said there was no danger to drinking water. She emphasized that E. coli had occasionally been found in the 30-kilometre stream before, and that it was not unusual for surface water to contain several types of bacteria. People are generally advised not to swim in streams and rivers in Hesse.
The ministries said there were various theories on how the E. coli got into the stream, though they added that the test sample was taken from near a sewage plant. While such plants generally have very high hygiene standards, authorities said this could not be ruled out as a possible source.
Two farms near the Erlenbach have permission to use its water, though only for potatoes and sugar beets, which are currently not in season.
More samples from the stream were sent for testing on Friday, with results expected in two or three days.