Demonstrators in Fretzdorf, some 100 kilometres (62 miles) northwest of Berlin, called for scrapping plans to use the site as training ground for low-flying military aircraft, which would also involve bombing runs.
They objected that the training activities would create noise pollution and drive away tourists. Organisers of the protest estimated their numbers at nearly 10,000. Opponents won an early victory last month when a court ruled against the army using the site, known locally as "Bombodrom."
Sunday's rally was part of a series of anti-military protests, as several German cities hosted demonstrations against nuclear weapons and the war in Afghanistan over the holiday weekend.
Twenty demonstrations were held in several cities including Munich and Berlin on Saturday, with protesters showing support for US President Barack Obama's goal of ridding the world of nuclear weapons.
The demonstrators also protested against NATO, which leads a 58,000-strong international force in Afghanistan that includes 3,500 German soldiers.
"The proposal of total nuclear disarmament is a central concern of the Easter Marches movement, which took to the streets for the first time in 1959 against the risk of nuclear war," said Peter Strutynski of the German Committee for Peace.
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More demonstrations are scheduled in Frankfurt and Hamburg on Monday.