Obama made the pledges aboard the Philippine Navy's flagship, shortly after arriving in Manila for a summit of Asia-Pacific leaders to also be attended by Chinese President Xi Jinping.
"My visit here underscores our shared commitment to the security of the waters of this region and to the freedom of navigation," Obama said as he announced the assistance.
The offers were aimed at reassuring allies that the United States was committed to maintaining security in the region's waters, following Chinese artificial island building in parts of the South China Sea.
The Philippines, Vietnam, Malaysia, Brunei and Taiwan have competing claims to parts of the sea, which is also believed to sit atop vast oil and gas resources.
China's building of artificial islands close to the Philippines prompted the US to deploy a missile destroyer and B-52 bombers to the area in recent weeks.
China was almost certain to react angrily to Obama's announcement, as it insists the United States has no right to involve itself in disputes over waters that are far away from US coasts.
In Beijing just before the US announcement, Chinese vice foreign minister Liu Zhenmin warned the other claimants that China could take control of the islands they occupy.
"The Chinese government has the right and the ability to recover the islands and reefs illegally occupied by neighbouring countries," Liu said.
"But we didn't do that, we exercised maximum restraint."
The Philippines, which has one of the weakest militaries in Asia and is the most vocal critic of China's actions in the sea, will receive the most support under the US package.
He said the Philippines would also get a research vessel to help map its territorial waters, while vowing US commitment to defend its longtime ally was "ironclad".
The Philippines will receive a record USD 79 million in assistance to bolster maritime security this financial year, the biggest recipient in Southeast Asia, the White House said.
