Mix, who worked on BP's unsuccessful attempt to stop the gusher using a technique called "top kill," had access to internal data about the amount of oil flowing from the well.
Justice Department prosecutor Jennifer Saulino said Mix received 10 separate notices that he was obligated to preserve everything related to his work. BP warned him repeatedly about the consequences of deleting messages, she added.
"This is a case about choices," Saulino said. "The defendant was told to do nothing, but he chose to do something."
McPhee said her client preserved and turned over documents and other records containing the same information that he allegedly tried to conceal.
"Kurt was focused on stopping the flow of oil, on cleaning up the oil, on making deep-water drilling safer," she said. "Kurt does not have a corrupt bone in his body."
The trial, which is expected to last up to three weeks, is scheduled to resume Wednesday with testimony from an FBI supervisor who worked on the investigation.
On May 26, 2010, the day the top kill attempt began, Mix estimated in a text to a supervisor that more than 630,000 gallons of oil per day were spilling three times BP's public estimate of 210,000 gallons daily and a rate far greater than what the company said a top kill could handle. That text was in a string of messages that Mix exchanged with his supervisor, Jonathan Sprague, before deleting it on Oct. 4, 2010.
"And he did it within days of learning those messages might be collected for legal proceedings," Saulino said.
Saulino described Mix as BP's "go-to guy" on flow-rate issues after the spill. She said Mix didn't share his higher estimates with a team of outside scientists during a May 2010 meeting, something Saulino suggested could have been his motive for later deleting his text message to Sprague.
Mix also allegedly deleted a string of text messages he exchanged with a BP contractor in August 2011, several weeks after federal authorities issued a subpoena to BP for copies of some of Mix's correspondence. The indictment also accuses Mix of deleting one voicemail from the contractor, one voicemail from Sprague and one voicemail from an unidentified caller that went through BP's general switchboard.
McPhee said there was nothing sinister about her client's deletion of the messages. She accused prosecutors of glossing over the fact that Mix also deleted a string of text messages with his sister.
"People delete text messages and voicemails all the time, for all kinds of innocent reasons, and sometimes for no reason at all," she said.
Each count of obstruction of justice carries a maximum penalty of 20 years in prison and a fine of up to $250,000.
Three other current or former BP employees await trials on spill-related criminal charges.
BP well site leaders Robert Kaluza and Donald Vidrine have pleaded not guilty to manslaughter charges stemming from the rig workers' deaths. Prosecutors say they botched a key safety test and disregarded troublesome high pressure readings before the blowout.
Former BP executive David Rainey is charged with concealing information from Congress about the amount of oil spewing from the well.