The Met Office has upgraded its weather warning for the Highlands and Islands from yellow to amber.
Forecasters are predicting prolonged and heavy rain tomorrow and Monday.
Lochaber and the Great Glen are expected to be the worst hit.
The Met Office also advise the public should be prepared for disruption due to flooding.
A number of west coast ferries have already been cancelled today.
The Scottish Government said that it, along with Transport Scotland, local authorities, Scottish Environment Protection Agency and Police Scotland, was closely monitoring the situation to make sure that all of the necessary preparations are being made for the conditions.
A Transport Scotland spokesman said: “The Met Office has issued an amber alert warning of heavy rain which runs from early tomorrow morning through until around midnight on Monday.
“This may lead to disruption on local roads and to ferry services. With the conditions we can also expect to see flooding in areas and road users should be prepared before they set off on their journeys. While we will do everything we can to mitigate the impacts, people travelling should be prepared and plan their journeys accordingly.
“A great deal of work has been undertaken to make sure that Scotland is prepared for any likely transport disruption, and we will continue to monitor events through our national control centre.
“Before heading out, we ask the public consider the conditions and listen to radio reports, visit the Traffic Scotland website or twitter feed, and consult their local travel operators.”