Three Mortar batteries were constructed beneath the ramparts of the fort. Each one held three 13-inch smooth bore mortars for intermediate range defence. These mortars fired a heavy projectile weighing 200 lbs at 45 degrees elevation to provide plunging shot that was to be employed against enemy siege works and breeching batteries.
The mortar batteries at Fort Nelson were not fitted with their mortars due to the fact that they were considered obsolete by the time Fort Nelson was finished. Also the crews found it difficult to observe the fall of their shot and had to rely upon messages sent down from the main ramparts before adjusting the charges to alter the range of the mortar. The mortars were superseded by howitzers that were placed in a more favourable position on the main ramparts.