His command in combat during the Second Boer War was criticised, but he achieved considerable success during his long life in his military and civil posts.

During the PEF Survey of Palestine he conducted one of the first major excavations at the Temple Mount in Jerusalem, thereby ushering in a new age of Biblical archaeology.

[3][4] Warren and his team also improved the topographic map of Jerusalem[5] and made the first excavations of Tell es-Sultan, site of biblical city of Jericho.

In 1876, the Colonial Office appointed him special commissioner to survey the boundary between Griqualand West and the Orange Free State.

He was then appointed special commissioner to investigate "native questions" in Bechuanaland and commanded the Northern Border Expedition troops in quelling the rebellion there.

He held this post until 1884, but it was interrupted in 1882, when the Admiralty sent him to Sinai to discover what had happened to Professor Edward Henry Palmer's archaeological expedition.

In 1883, he was also made a Knight of Justice of the Order of St. John of Jerusalem, and in June 1884 he was elected a Fellow of the Royal Society (FRS).

In December 1884, by now a lieutenant-colonel,[13] Warren was sent as HM Special Commissioner to command a military expedition to Bechuanaland, to assert British sovereignty in the face of encroachments from Germany and the Transvaal, and to suppress the Boer freebooter states of Stellaland and Goshen, which were backed by the Transvaal and were stealing land and cattle from the local Tswana tribes.

At Queen Victoria's Golden Jubilee in 1887, the police received considerable adverse publicity after Miss Elizabeth Cass, an apparently respectable young seamstress, was (possibly) mistakenly arrested for soliciting, and was vocally supported by her employer in the courts.

To make matters worse, Colonel Warren, a Liberal, did not get along with Conservative Home Secretary Henry Matthews, appointed a few months after he became Commissioner.

Matthews accepted Monro's resignation, but simply moved him to the Home Office and allowed him to keep command of Special Branch, which was his particular interest.

In his book, Abberline: The Man Who Hunted Jack the Ripper, author Peter Thurgood indicates that Warren was criticised during the investigation.

[15] As recently as 2015, a book about the Ripper case by Bruce Robinson castigated Warren as a "lousy cop" and suggested that a "huge establishment cover-up" and a Masonic conspiracy had been involved.

In its book review, The Guardian stated that "most historians put the police's failure to catch the Ripper down to incompetence" but did not specifically name Warren in this context.

[18] Watermanship being one of the many skills required of the Sapper led to the formation of a sailing club at the School of Military Engineering in 1812 and later to the development of cutter rowing teams.

The Sapper teams were drawn from members of the Submarine Mining School, but when the service was disbanded in 1905, the tradition of cutter rowing was continued by the fieldwork squads.

By then, Warren was 59 years old, was said to have a "disagreeable temper", had little recent experience leading troops in battle and did not get along with his superior, General Sir Redvers Buller.

At the Battle of Spion Kop, on 23–24 January 1900, he had operational command, and his failures of judgment, delay and indecision despite his superior forces culminated in the disaster.

A book by South African author Owen Coetzer attempted "in a small way to vindicate him" for his Boer War actions.

[23] He was also involved with another group, the Church Lads' Brigade [24] and 1st St Lawrence Scout Group, then called 1st Ramsgate – Sir Charles Warren's Own Scouts [25] He had previously authored several books on Biblical archaeology, particularly Jerusalem, and also wrote "On Veldt in the Seventies", and "The Ancient Cubit and Our Weights and Measures".

He died of pneumonia, brought on by a bout of influenza, at his home in Weston-super-Mare, Somerset, was given a military funeral in Canterbury, and was buried in the churchyard at Westbere, Kent, next to his wife.

He was played by Anthony Quayle in the 1979 film Murder by Decree, which features the characters of Sherlock Holmes and Doctor Watson in a dramatisation of a conspiracy theory concerning the Ripper case.