The bodies of the victims - one of whom was the suspect's ex-girlfriend - were discovered by a cyclist at the source of the Huecar river near the town of Palomera in central Cuenca province on Wednesday.
The bodies had been covered in quicklime and showed burn marks as a result, in what appeared to have been an attempt to speed up their decomposition, local media reported.
The women have been identified as 24-year-old Laura del Hoyo and 26-year-old Marina Okarynska. They had been missing since August 6, the same day the suspect, Sergio Morate, was last seen.
An international warrant was issued for Morate's arrest and after several days on the run he was apprehended in western Romania, Spain's interior ministry said in a statement.
"The arrest took place at a residence in the Romanian city of Lugoj in the Timisoara region," it said. Two Romanian men who were with him at the time were also detained.
The suspect who is believed to be "responsible for the death of two young women" will be transferred to Spain "as soon as possible", the statement added.
Morate's family had earlier taken to Facebook to distance themselves from him and accuse him of the murders.
"We don't know what kind of devil or terrible madness possessed you but you must know that not only did you kill these girls but also their families and your own," they wrote on Wednesday, in a statement that was also sent to the media.
The daily El Pais reported that the suspect had already served time for detaining and assaulting another former girlfriend.
He had recently told people close to him that he wanted to go to a country that did not have an extradition treaty with Spain, according to the newspaper.