He excavated a number of sites in the Nile Delta including Tell el-Maskhuta (1882), the Wadi Tumilat (1885–86), Bubastis (1886–89), Tell el-Yahudiyeh (1887), Saft el-Hinna (1887), Ahnas (1890–91), Mendes and Tell el-Muqdam (1892).

In the 1890s he excavated at the Mortuary Temple of Hatshepsut at Deir el-Bahri where he was assisted by David George Hogarth, Somers Clarke and Howard Carter.

In 1873, he married Marguerite de Pourtalès who accompanied him on his 14 trips to Egypt, meticulously recording his finds in photographs and drawings and including detailed accounts of the expeditions in her diaries.

Naville was an archaeologist of the old fashioned school that concerned itself with large scale clearance of sites and little regard for the detailed evidence possibly to be found in the course of excavation.

In his lifetime he was criticized by W. M. Flinders Petrie for his archaeological methods and D. G. Hogarth was sent by the Egypt Excavation Fund to observe and report on the nature of his work at Deir el-Bahri.