The tourists had taken the picture at Bangkok's famous Wat Arun temple and posted it on Twitter and Instagram.
Thailand has very strict laws on behaviour considered disrespectful and offensive to its Buddhist religion.
The two tourists were held late on Tuesday when trying to leave the country at Bangkok's Don Mueang airport.
Deputy spokesman of the Thai immigration police, Col Choengron Rimpadee the two had been on a watch-list after authorities had spotted the controversial social media post.
"Once they are through with the charges, the Thai immigration police will revoke their visas and push for deportation," he said. "They will also be blacklisted from coming back to Thailand."
He explained the two were brought to Bangkok Yai police station to be charged with public nakedness, an offence liable for a fine of up to 5,000 baht ($153; £115).
However, other Thai government and police officials have told media that the charges could be more serious.
The San Diego Gay and Lesbian News quoted a San Diego city commissioner as saying the men had asked for help.
The commissioner, Nicole Murray-Ramirez, told the paper: "Though I am very disappointed in their actions, I am talking to US government officials to see what assistance we can give them."
People visiting Buddhist sites in Thailand are expected to dress modestly and signs advise them to cover their shoulders and legs.
Tourists are also told to not buy statues or images of Buddha as souvenirs.
In 2015, four European tourists received jail terms and fines in Malaysia for posing semi-nude on Mount Kinabalu, which is considered sacred.
Also in 2015, two American women were arrested, fined and deported for taking nude photographs inside Cambodia's Angkor Wat complex.
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