You might consider waterbody but it is a less common word and it is often spelled as water body. It covers small bodies of water too but it depends on the context also.
A body of water or waterbody is any significant accumulation of water, generally on a planet's surface. The term body of water most often refers to large accumulations of water, such as oceans, seas, and lakes, but it includes smaller pools of water such as ponds, wetlands, or more rarely, puddles
Although Lake Victoria is a very useful waterbody for transport, a floating vegetation known as hyacinth is threatening its existence.
[Peak Revision K.C.S.E. Geography By M. W. Magu]
Though, you can consider waterway also:
A waterway is any navigable body of water. A shipping route consists of one or several waterways. Waterways can include rivers, lakes, seas, oceans, and canals.