Arriva Trains Wales routes between Aberystwyth and Shrewsbury were cancelled on Monday morning due to high river levels at Machynlleth, Powys.
Some services from North Llanrwst to Blaenau Ffestiniog were also delayed due to speed restrictions on the line.
One flood warning and several flood alerts remain in place for north east, north west and mid Wales.
Meanwhile, 300 homes left without power after storms at the weekend have been reconnected.
Scottish Power said services to homes in north Wales were affected by very strong winds, which damaged power lines and brought down trees.
Power was reconnected at 18:30 GMT on Sunday.
A further 259 Western Power Distribution customers were also without electricity in the Pontyberem area of Carmarthenshire.
A spokesman for SP Energy Networks said: "We apologise for any inconvenience caused. Our engineering teams worked hard in poor conditions to restore supplies as quickly as possible."
Train services disrupted in mid and north Wales due to flooding and poor weather conditions have resumed.