In Anno1404, you could build docks (or maybe something else, I am not sure I remember correctly), each of which would increase the capacity of the warehouse. I couldn't find anything equivalent in Anno2070. Is it possible to increase warehouse capacity (apart from upgrading it) ?
The building that you're looking for that equates to the docks in 1404 is the Harbor Depot. In addition to being able to upgrade your Port Authority Warehouse by clicking in the top right corner, you can build these buildings. They'll store 40 more tons of goods.
Click on the warehouse (your main one at the docks), in the top right (where you can choose how much things to move) of the little warehouse menu (where it shows all the goods), there is a little house icon with a plus next to it.