The proportion of trains arriving within five minutes of schedule fell by more than 3 percentage points compared to a year ago, with 86.5 per cent of trains on time.
ScotRail said the downpours cancelled out improvements that would otherwise have seen performance rise for a third month.
It said Edinburgh and Glasgow saw more than three times their usual February rainfall.
During Storm Dennis, the Inver Viaduct north of Dunkeld was closed after the River Braan rose above safety markers on 15 February, halting Perth-Inverness trains.
Other troublespots included a reservoir aqueduct overflowing onto the line at Bishopton in Renfrewshire the following day, forcing overhead wires to be switched off.
On 24 February, high river levels in the Allan Water stopped trains near Dunblane because of the threat to the Mill O’Keir Viaduct.
The operator’s February punctuality was last lower in 2005, when it sank to 85.7 per cent.
The poor weather accounted for a 4 point drop in punctuality over the four weeks to 29 February.
ScotRail said it would otherwise have topped 90 per cent for the first time since June 2019.
The significant dent in performance also hit ScotRail’s annual punctuality figure, on which it is officially measured by the Scottish Government.
This “moving annual average” dipped by 0.3 points to 88.2 per cent compared to January, which is more than 4 points below target.
Scottish Conservatives transport spokesman Dean Lockhart said: “It’s important to recognise the incredibly hard work of all rail workers who helped to keep services running in the face of very challenging weather conditions.
“The drop in the PPM is disappointing but is largely explained by adverse weather.
“That said, we need more significant investment to increase the resilience of the network in response to challenging weather.”
Paul Tetlaw, policy forum convener of sustainable transport campaigners Transform Scotland, said: “The latest flooding and the impact on ScotRail services should further focus minds in government.
“There is an urgent need to invest in sustainable transport modes and not further road building which simply generates more car use.
“The rail network north of the Central Belt is in urgent need of modernisation and city transport systems should prioritise sustainable modes.
“Beyond that the rail network must be protected from the weather extremes which are now becoming the norm.”
Alex Hynes, managing director of Scotland’s Railway, which also includes Network Rail Scotland, said: “This was an exceptionally challenging period and unfortunately the weather prevented us delivering the level of service our customers expect and deserve.
“Our people across the country worked flat out and did everything possible to keep services moving.”
ScotRail expects to meet its 92.5 per cent moving annual average target by 2022 – which now coincides with the early end of operator Abellio’s franchise.