A pumping station is a vat built to pump water from an underground location. It also contains a water purifying element.
Colonies often had to build these to collect water to drink. For example, the Federation colony on Tau Cygna V built one and were very proud of it. This particular station was disabled by Data with a single phaser burst in order to demonstrate to the colonists that they could not hope to stand against the Sheliak who had a claim on the planet. The destruction of the pumping station was thus the catalyst for the resettlement of the colonists. (TNG: "The Ensigns of Command")