This made for a real crappy commute.

A nasty clogged-up toilet and nature calling for a pair of MTA workers during Friday’s morning rush-hour snarled subway service on five different lines, according to the transit agency and a report.

The double bathroom break caused temporary service changes on the A, C and E lines and prompted delays on those lines, as well as hold-ups on the F and M lines, the MTA said.

MTA spokesman Shams Tarek told The Post that two employees on the A and C lines “needed emergency bathroom breaks” at “around exactly the same time during rush-hour.”

At 8:35 a.m. the urge hit an operator at a Manhattan control tower at 42nd Street and 8th Avenue with a busted toilet — and about 10 minutes later the operator of a C train stopped at Brooklyn’s Jay Street-MetroTech station to sit on the throne, Tarek said.

“The tower operator needed to use a bathroom farther away than usual because the one in the tower recently went out service for repairs and was not restored yet,” said Tarek.

The website Jalopnik, citing a source, reported that a toilet in that tower has been backed up for three days and was the main culprit behind the morning service disruptions.

A transit source said the toilet issue was much more involved than a clog.

There was a problem with the electric pump system that the toilet relies upon to work and it needed to be repaired, the source said.

The toilet was fixed and returned to service by 2 p.m. Friday, the MTA said.

The MTA’s NYCT Subway Twitter account tweeted at 8:42 a.m. that there would be service changes “while our crew takes a pit stop.”

One curious straphanger then replied to the tweet asking: “what does this even mean?” to which the NYCT Subway account tweeted back at 9:17 a.m.: “Hi there. A member of the train crew needed a restroom break. They have since gotten back on their train and are getting on the move.”

Twitter user @mullymt tweeted back, writing: “I appreciate the honesty, at least.”

Another user, @jasondeth, quipped: “So there was a movement during a no movement period.”

During the disruptions, trains on the C line ran express from Canal Street to 59th Street-Columbus Circle in both directions, while northbound E trains ran on the F line from West 4th-Washington Square to Jackson Heights-Roosevelt Avenue.

Normal train service resumed by about 9 a.m., the MTA said.

“We thank our customers and colleagues for their patience and understanding,” Tarek said.

The matter highlighted just how tricky it is for MTA train operators and conductors when they need to relieve themselves on the job.

“Comfort breaks are a problem throughout the subway system and on the buses too,” Jim Gannon, a spokesman for the Transport Workers Union told The Post.

Gannon said some MTA towers where operators work “are kind of remote” and some could have only one person manning them at a time.

If a train operator has to use the john “they’ll call a rail control center and they’ll pull into the next station and they’ll secure the train and they’ll go,” Gannon said, adding “they’ll get back as soon as they can.”