He has pleaded not guilty to all of the charges, none of which are directly related to work he performed for Mr Trump's campaign.
Judge Jackson was not moved by any of Mr Manafort's assertions.
"Paul Manafort maintains his innocence and looks forward to prevailing in this matter", his spokesman, Jason Maloni, said in an email.
Judge Amy Berman Jackson roundly rejected Manafort's motion to dismiss the special counsel's indictment, citing several examples of legal rectitude for Mueller's aggressive investigation of Russian meddling during the 2016 presidential campaign.
Paul Manafort, who has been charged with money-laundering conspiracy, false statements and acting as an unregistered foreign agent, argued Mueller exceeded his authority as the case was unrelated to Russian election interference.
"Manafort was an obvious person of interest", U.S. District Judge Amy Berman Jackson wrote in part of her 37-page opinion.
"The indictment falls squarely within that portion of the authority granted to the Special Counsel that Manafort finds unobjectionable: the order to investigate 'any links and/or coordination between the Russian government and individuals associated with the campaign, '" Jackson wrote.
The special counsel's office declined to comment on Jackson's memorandum opinion.
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Manafort faces a separate trial set for July 10 in Alexandria, Virginia.
"None of it had any relation to the campaign", Ellis said during the April 4 hearing. It was logical and appropriate for investigators tasked with the investigation of "any links" between the Russian government and individuals associated with the campaign to direct their attention to him. Additionally, Rosenstein "confirmed in writing that he assigned the Special Counsel the specific responsibility to investigate the very allegations that comprise the" challenged indictment.
Finally, Mueller was appointed "to take over an existing investigation".
Second, even if Mueller had exceeded his authority, the regulations governing appointments of special counsel provide that they "are not meant to, do not, and may not be relied upon to create any rights, substantive or procedural, enforceable at law or equity, by any person or entity, in any matter, civil, criminal, or administrative".
Those regulations, Jackson said, "place no boundaries on who can be investigated or what charges can be brought-what they address is who decides who the prosecutor will be". She cited not only the May 2017 appointment order, but also an August 2, 2017, memo by Rosenstein that further detailed the responsibility given to Mueller.
The cases are U.S. v. Manafort, 18-cr-83, U.S. District Court, Eastern District of Virginia (Alexandria), and U.S. v. Manafort, 17-cr-201, U.S. District Court, District of Columbia (Washington).
Deputy Solicitor General Michael R. Dreeben had defended the investigation, arguing last month in the District that prosecutors would naturally want to scrutinize Manafort's long-standing ties to Russian-backed politicians, financiers and others and whether any served as "back channels to Russia".