Ben Bernanke won the backing of the Senate for a second four-year term as chairman of the Federal Reserve by a comfortable margin Thursday. Even with that storm behind him, Mr. Bernanke faces formidable political and economic challenges made tougher by the bruising confirmation fight.

Weeks of criticism from Congress—and moments during which his confirmation prospects seemed uncertain—have weakened Mr. Bernanke's political standing. That may make it harder for him to defend the Fed as Congress prepares to intensify its oversight of monetary policy and curb the Fed's authority over the banking system. In an interview, Mr. Bernanke's predecessor, Alan Greenspan, called his own occasionally tense relations with Congress "tranquil" by comparison.

The intense scrutiny of Mr. Bernanke's record underscored risks to the Fed's cherished independence to change interest rates without political interference. That independence is key to retaining financial markets' confidence in the central bank.

Fed officials "are going to be fighting a rear-guard action against congressional encroachment and interference," says Martin Barnes, managing editor of BCA Research Inc., an investment research firm.