The controversial project seemed to receive a boost last week when an environmental impact report from the State Department concluded the pipeline would not have much effect on global warming, which was a major concern for the Obama administration.
The report was seen by some Keystone supporters as a green light for Washington's approval of the project.
"The president's role is now is to protect this process from politics," McDonough said on CBS' "Face the Nation. "Let the expert agencies and the Cabinet secretaries make their assessments both of the study that was put on Friday as well as its impact on the national interest. So we'll resolve that over the coming period of time."
McDonough said the administration remained committed to pushing back on climate change. "California is now seeing some pretty serious developments as a result of climate change, so we will be looking at that," he said.