In his strongest remarks on the issue yet, Mr Obama said climate change would "impact every country on the planet".
The US president made his comments in a speech to students at the Coast Guard Academy in Connecticut.
He has previously identified climate change as a central issue for the remainder of his time in office.
Faced with strong opposition on the issue from Republicans and industry, Mr Obama used his speech to frame the threat in terms of national security.
He said: "I'm here today to say that climate change constitutes a serious threat to global security, an immediate risk to our national security and make no mistake: it will impact how our military defends our country.
"Denying it or refusing to deal with it endangers our national security. It undermines the readiness of our forces."
He went on to list specific military facilities seen as under threat from adverse weather conditions.
"Around Norfolk, high tides and storms increasingly flood parts of our Navy base and an air base. In Alaska, thawing permafrost is damaging military facilities.
"Out West, deeper droughts and longer wildfires could threaten training areas our troops depend on."
He told the Coast Guard Academy students: "You are part of the first generation of officers to begin your service in a world where the effects of climate change are so clearly upon us.
"Climate change will shape how every one of our services plan, operate, train, equip, and protect their infrastructure, today and for the long term."
Mr Obama has used executive orders on climate change to circumvent opposition in Congress - issuing one in March ordering federal agencies to cut greenhouse gas emissions.
In China last year, he committed to reducing US carbon emissions by 26-28% by 2025, and he will travel  to Paris in December for an international summit on greenhouse gases.
President Obama has called climate change "a serious threat to global security" and heavily criticised climate change deniers.