State-owned Caledonian MacBrayne also saw falls in coach and commercial vehicles.
The company, which receives a £73 million subsidy from the taxpayer, said the big increase in passengers and cars in 2013 came despite losing nearly 1200 sailings due to bad weather in the last two months of the year.
Annual carryings for January to December 2013 showed 4,594,520 passengers and 1,064,324 cars travelled with CalMac on its 27 routes, with 18 routes showing an increase in traffic.
Two routes were trialed for the first time in 2013 - the Ardrossan-Campbeltown summer service which began in May, and the Lochboisdale-Mallaig winter service, which began in November but has been badly affected by the extreme weather.
In fact more sailings were cancelled on the Lochboisdale-Mallaig run than completed - the route carried just 434 passengers, 162 cars and 22 commercial vehicles by the end of the year.
CalMac Operations Director Brian Fulton said: "2013 was a year of very mixed fortunes.These storms continue to have a devastating effect on sailings right across the network."