Train drivers' union Aslef condemned the "unacceptable" state of the 1046 from Aberdeen to Glasgow.
It is one of an inter-city fleet whose upgrade has been delayed because of problems at refurbishment firm Wabtec.
Pictures showed buckets positioned in the aisle beside seats on the "High Speed Train" (HST), which used to run in the west of England.
Another was said to show mould growing in a carpet.
It is claimed staff were forced to operate the service despite alerting control staff.
ScotRail said the control room was unaware of the problem until the train left Aberdeen.
However, it was unable to explain why there were buckets on the train.
A rail source said: "These photos were taken today on board an HST that left Aberdeen going to Glasgow.
"Buckets all over catching water that's leaking into the coach.
"The last pic is actually mould growing on the side carpet - disgusting.
"Just pointing out the level of cheap, nasty trains we are required to work on ScotRail."
The revelation came after it emerged ScotRail will not meet a deadline for ending the disposal of toilet waste onto tracks by the end of the year because of the refurbishment delays.
Only eight of ScotRail's planned fleet of 26 HSTs have been upgraded so far, forcing it to run 11 in their "classic" state.
Aslef Scotland district organiser Kevin Lindsay said: "It’s disgusting that Scotrail’s HST trains spew raw sewage on to the tracks, but to now run trains with no toilets, rain having to be caught in buckets and mould growing on carpets is just unacceptable.
"Passengers on this service should be given a full refund and a personal apology from Abellio ScotRail.
"The Scottish travelling public deserve better.
"It’s time for the Scottish Government to stand up for the people of Scotland and strip the discredited Dutch railway firm Abellio of the franchise and return ScotRail to public ownership.”ScotRail said the buckets were to deal with "water ingress from the ceiling" and the train would be fully checked over in a depot tonight.
The train operator said its control team did not become aware of the condition of the carriage until after the train had left Aberdeen.
It then arranged for a technician to board the train when it reached Perth - one and a half hours later.
A second technician met the train at Glasgow Queen Street "to carry out the necessary repairs", accompanied by a cleaning crew.
A ScotRail spokesperson said: “As soon as we were made aware of the faults within the carriage, we arranged for technicians and our train presentation team to meet the train and carry out the necessary repairs.”