If it was possible to transport by water, then, yes it was always (and still is) the cheapest way to move goods.
It has not always been, and is not, always the preferred way.
Today, 90% of world trade by volume is carried by water. 70% of world trade by value is carried by water.
Source: https://people.hofstra.edu/geotrans/eng/ch3en/conc3en/ch3c4en.html
Most of world trade is carried by water, because water transport is by far the cheapest way to move cargo. That a lesser percentage is carried by value than by volume, indicates that sometimes other ways of moving goods are preferred (especially for high value cargoes).
The disadvantages of water borne transport are:
It is slow. Ships have traveled at average speeds from circa 4 knots (in the early days of sail) to circa 15 knots today. Trucks and trains are faster, and airplanes much faster. (Back before the railroad, nothing was much faster than ships, especially as ships could keep sailing 24 hours a day, while most other forms of transport had to stop for the night.) Perishable or urgently required goods are often worth transporting by air or train or truck, rather than by sea.
It requires considerable up-front investment. Ships are pretty expensive to build compared to wagons or trucks or trains or airplanes. Unless a trade route is going to be used extensively, it might not be worth investing in ships, (though, of course, cheaper, smaller ships, or boats, or canoes might be employed on such routes).
Higher value cargoes (especially, higher comparative value cargoes, or higher profit margin cargoes) can afford to pay more in transport costs and still make a profit after being shipped. These high value cargoes are more likely to be shipped by air or land if they are perishable or urgent.
Water transport can only go where there is water. Other transport must be used where navigable water does not exist.