China asserts sovereignty over almost all of the strategically vital waters in the face of rival claims from its Southeast Asian neighbours.
In his speech to the UN General Assembly on Tuesday, Trump decried "threats to sovereignty" in Ukraine and the resource-rich South China Sea, without explicitly mentioning Russia or China.
"We must uphold respect for law, respect for borders, and respect for culture, and the peaceful engagement these allow," Trump said.
China asserts sovereignty over almost all of the strategically vital waters in the face of rival claims from its Southeast Asian neighbours, and has rapidly turned reefs into artificial islands capable of hosting military planes.
The United States has conducted three "freedom of navigation" operations near islands held by China to challenge Beijing's maritime claims since Trump took office in January.
"For some time now, some countries have used the pretext of freedom of navigation to bring their planes and fleets near the South China Sea," Chinese foreign ministry spokesman Lu Kang said Wednesday.
"Actually, I think this is behaviour that has threatened the sovereignty of South China Sea countries," Lu told a regular news briefing.
Lu said the situation in the sea "has been cooling down" thanks to efforts by China and the Association of Southeast Asian Nations.
"I hope that this situation can be respected by relevant countries," he said.
Lu reiterated Beijing's call for efforts to bring the nuclear issue "back to the right track of peaceful settlement through dialogue and consultation."