The speed restrictions are due to cause ‘some delays’ and are in place to ensure safety across Scottish train tracks as torrential downpour continues to affect travel.
There are 'blanket' speed restrictions in place until 8am on Monday between Keith and Elgin and Dunkeld and Blair Atholl.
In the West of Scotland, there is also a 40mph speed limit because of the weather in force until 11.59pm on Saturday evening.
This will be between Glasgow Queen Street and Croy, and also between Garnqueen North Junction (near Gartcosh) and Sighthill East Junction (near Springburn).
A Network Rail Scotland spokesperson said: “We're constantly monitoring the weather and the impact it's having on the network in real-time, thanks to our dedicated forecasters and monitoring equipment.
"Right now, there's a number of speed restrictions in place across the country due to the heavy rain we've seen.
"The speed restrictions currently in place due to the weather will, unfortunately, cause some delays. We're sorry if this affects you.”
The news comes as a yellow weather warning of rain and thunderstorms remains in place across Scotland until midnight on Sunday across most of the country, including all of the central belt.
Forecasters said some areas could be lashed by 20 to 30mm of rain over the space of an hour on Saturday after 40 to 60mm of rain fell in parts on Friday. Glasgow was hit by flash flooding after downpours on Friday.
Over the course of this weekend several places could be hit by 50-80 mm building up.
Many of the showers and thunderstorms will ease on Sunday evening but there is a small risk of heavy rain persisting into Sunday night in a few places, according to the Met Office.
A Met Office Spokesperson said: “Heavy rain is expected to develop in some areas overnight, Sunday then expected to bring further slow-moving heavy, thundery downpours.”
While there will be sunny spells among the showers, temperatures are set to be on the cooler side for this time of year, predicted to be in the high teens to low 20s.