Security was handled much the same way as it was for the municipal parts of the Wall. There were concrete walls and barriers on the eastern zone's river banks, which this picture and this one show. There were also some underwater obstacles and barriers the Grenztruppen placed in areas that were easy to cross. Bernd Lehrmann was one victim of these obstacles. The GDR also militarized the waterways on its side of Berlin and enforced a rigid discipline for both East and West water traffic. This contributed to the death of the four-year old West Berlin boy Cengaver Katrancı who fell into the Spree on 30 October 1972. The West Berlin fire department could not intervene lest it be shot at by the Grenztruppen if it went in without GDR authorization and the local GDR boats would not engage in a rescue attempt because the Western banks were forbidden zones.

The watercourses were a weak point though in the Wall and a number of escapees recognized this. Unlike land routes, it was unfeasible to create a death strip of mines as these would have been harder to detect for GDR water traffic. But the Grenztruppen's patrolling of its waterways did become more sophisticated by the 1970s. The Grenztruppen added speedboats to their arsenal starting in the late 1960s. These boats would try to intercept escapees as seen in this 1988 video of a river crossing. These boats would patrol the waterways and swiftly respond to any sightings or reports of crossings. Even though sealing off water access involved greater difficulties than overland routes, the GDR was more than up to the task of making a water escape as deadly as possible for those who wished to leave the workers' and peasants' state.