A number of naval battles have been fought at the mouths of the Nile. Most notably the Battle of the Nile during the Napoleonic Wars, but Plutarch also mentions naval actions at the mouth of the Nile in Alexandria in 39, B.C., when Antony's remaining ships deserted to Octavian and he committed suicide. It's unclear, though, whether there was actually any fighting on the river itself, or whether Antony's ships all deserted past the mouth on open waters--in any case, Octavian's ships landed their troops on the Nile, which I think counts. Ramesses III repulsed a naval invasion by some of the Sea Peoples sometime between 1180 and 1170, B.C. Naval warfare on the Nile is well-attested in Egyptian iconography from a very early date, and during the New Kingdom there was an impressive royal military dockyard near Memphis at Peru-nefer, built by Thutmose III.

In the modern sense of naval warfare operations, not really. However, as the primary thoroughfare between upper and lower Egypt, and Egypt to Nubia/the Mediterranean, it was certainly not uncommon to use the Nile as a means to transport soldiers (they didn't always just march) and to transport supplies to distant armies.