The deals come as Kerry travels to Asia meeting with governments and discussing environmental issues.
He was in the Indonesian capital Jakarta for the announcement.
Calling Indonesia's biodiversity the "richest in the world," Kerry said a deal to combat the spread of foreign species into new ecosystems "really summons an obligation by all of us to try to do better." The memorandum of understanding also targets wildlife trafficking, the U.S. State Department said.
The second memo deals with supporting human rights in third world countries and emerging democracies.
Kerry and Indonesian Foreign Minister Marty Natalegawa said the cooperation between the two countries on such topics has increased over the years and noted the nations are the world's second- and third-largest democracies in the world.
The meeting wasn't without its bumps, however. Reporters questioned Natalegawa on his response to a weekend New York Times article alleging the Australian government, in conjunction with the U.S. National Security Agency, eavesdropped on communications between the Indonesian government and a U.S. law firm advising it on international trade negotiations.
Natalegawa had somewhat stern words for Australia over the allegations.
He questioned why, if the Australian spying policy is meant "to save Australian lives, to save the lives of other people," they were interested in conversations with lawyers about shrimp exports.
"I find it a bit mind-boggling, a little bit difficult, how I can connect or reconcile discussions about shrimps and how it impact on Australia security," Natalegawa said.
Kerry, for his part, reiterated the U.S. policy that eavesdropping is limited to matters of national security and not economic benefit for the U.S. government or private corporations.