Aksana Panova of the Ura.ru news agency in Yekaterinburg faces up to 15 years in prison if convicted on all the charges filed against her, the official Russian news agency RIA Novosti reported.
Her website, founded in 2006, has published stories about corrupt officials and police officers involved in shady deals in the Urals region.
The region is one of Russia's leading oil producers and a major industrial center.
Ura.ru has won praise as one of the few independent news sites to survive in Russia despite a Kremlin-led effort to silence government critics.
At the start of her trial Wednesday, Panova admitted withdrawing $400,000 from her website's bank account and transferring it to fictitious companies.
However, she testified the funds were used to pay staff salaries, something Russian businesses often do to avoid hefty welfare payments.
The 39-year-old mother also denied extorting money from a businessman in exchange for not publishing defamatory stories about him.