The warning reads that accumulations of 20-30 mm are likely in a few hours with a chance of up to 40 mm in one or two places, chiefly across higher parts.
There will be gale force Southerly winds with fallen leaves adding to the risk of flooding and possible disruption to transport.
The rain is expected to clear to showers early by mid-afternoon.
The forecaster warns that bus and train services will likely be affected with journey times taking longer – and tricky conditions on the road with spray and flooding probably making journey times longer.
The strongest winds are likely to be the southerlies ahead of the front, with gusts of 65 to 70 mph in coastal parts and perhaps 75 mph around the Northern Isles.
The coastguard in shared an image from the Baleshare Causeway North Uist with the causeway closed as a result of the extreme weather.