Nagura stones are smaller sharpening stones constructed in a similar way to other Japanese water stones. They are used to dress the surface of a water stone of the same grit or finer, removing abraded material that can become embedded in the stone.
In the later stages of sharpening at higher grits, a Nagura stone can be used to raise a slurry on the water stone that can be worked to break down the abrasive particles, improving the finish and polish of the blade.
Please note that each grit of Nagura stone is for use on similar grits of water stones or higher. The #1000 stone is used for dressing #1000 stones or higher, while #3000 and #5000 can be used to raise slurry on similar- or finer-grit stones.