The boats were pursued by German police in a dramatic 10-minute chase.
Activists in one of the boats brandished a large yellow banner that read: "G8 act now!" just as police caught up with them.
A second boat collided with another as it tried to outmanoeuvre the police, causing its four occupants to fall into the water a short distance from the shoreline, according to television images.
Two of the activists were injured, a Greenpeace spokesman said.
"In view of the crisis on the issue of climate protection, we want to hand over a petition to the summit," Greenpeace's climate expert Karsten Smid told AFP.
Smid said that protesters had used 11 inflatable dinghies in all, but most of them had been intercepted by the police and driven away from the maritime exclusion zone.
But at least two boats succeeded in penetrating the area.
"It must be possible to demonstrate peacefully," Smid said.
The summit has already been hit by anti-globalisation protests who blocked roads to the summit venue where the leaders of Britain, Canada, France, Germany, Italy, Japan, Russia and the United States were discussing climate change and aid to Africa.
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