Police spokesman Prawut Thawornsiri said the suspect appeared in a security video that shows a blurry image of an unidentified man in a blue shirt kicking a bag into the water near a busy pier on the night of August 17, soon after the explosion at the Erawan Shrine.
An explosion took place near the spot about 18 hours later on August 18, but caused no casualties.
Police have not determined a clear motive for the shrine bombing, which injured more than 120 people in addition to the 20 fatalities.
Possible suspects include Muslim separatists from southern Thailand, parties seeking to avenge the forced repatriation of ethnic Uighurs to China by the Thai government, opponents of Thailand's military government and feuding factions within the security services.
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The warrant issued today by the South Bangkok Criminal Court says the suspect in the river blast faces charges of attempted premeditated murder, exploding a bomb that could cause harm and unauthorised possession of explosives, Prawut said.
Police have not definitively linked the two blasts according to their public statements.
They have said a network of people must have been involved in the shrine bombing. An arrest warrant was issued last week for a suspect in that explosion, also without a name or nationality. No arrests have been made in either case.
Criticism of the police investigation has been strong because few facts have been clearly established, including the type of explosives used in the bombs.