Conwy Valley train services north of Llanrwst were hit due to flooding on the line but services resumed on Monday evening.
A flood warning is also in place for the River Conwy between Llanrwst and Trefriw.
Earlier, the Met Office issued a "be aware" warning for rain across Gwynedd, Conwy, Denbighshire and Powys.
Forecasters said rivers in Snowdonia were "swollen" after up to 2.5in (63mm) of rain fell over 36 hours in some areas.
However, the weather was expected to improve through the early evening.
A further nine flood alerts across Wales have also been issued.
Arriva Trains Wales said buses had replaced trains between Shrewsbury and Machynlleth due to flooding between Newton and Machynlleth on Monday evening.
In Trefriw, the B5106 has been closed in both directions due to flooding between Gower Road and Jubilee Road.
Rail services have been disrupted and motorists are being warned of flooding after heavy rain in parts of Snowdonia.