How can I build on top of lakes?

Solution 1:

Before 0.13 there was no way to cross bodies of water in vanilla Factorio. There were a couple of mods with different solutions.

A lot of players argued that building with the lay of the land is a nice challenge and give your factory "character" and makes it unique.

Other guys just wanted to build a massive factory and then use the mods to help them cross it.

Since 0.13, you can research the "land fill" technology and then use it to replace water with soil.

Solution 2:

With the release of version 0.13, researching the landfill technology will let you construct a landfill item that replaces water with grass. It costs 20 stone to create and builds in half a second.

Unfortunately there is no equivalent item to turn land into water, so be careful not to deprive yourself of locations for water pumps!