After the June troop build up and reorganization of the Schutztruppe into two regiments, Estorff was given command of a battalion of three companies in Lieutenant Colonel Mueller's 1st Field Regiment.
During the Waterberg campaign, Estorff's command consisted of 26 officers, 247 enlisted men, four artillery pieces and four machine guns. According to German sources*, Section von Estorff contained 3 Schutztruppe companies from the 1st Field Regiment. These were the 1st Field Company under Hauptmann Graf zu Solms-Wildenfels, the 2nd field company under Oberleutnant Franz Hermann Ritter, and the veteran 4th Field Company under Hauptmann Franz Ritter von Epp. He had native auxiliaries as well, from the Rehoboth "Bastards", under Oberleutnant Böttlin.
For artillery Estorff had the 3rd Field Battery with its C73 field guns under Oberleutnant Bauszus, and a machine gun section of 4 machine guns under Leutnant Graf von Saurma-Jeltf. The records indicate a radio section as well, although the main means of communication at in this campaign was via heliograph so perhaps that is what was indicated.
Estorff's section was detailed to advance of the Herero below the Waterberg from the East, and fought an action at Otjosongombe where his artillery was used to good effect. After the fighting at the Waterberg, Estorff's Section was tasked with pursuing the Herero through the Omaheke Sandveld, and it was this experience and the extermination order given by Lieutenant General von Trotha that Estorff felt seemed both extreme and unwise:
"crushing the people like this was in equal measure cruel and insane. One could have saved many of them and their herds, if one had spared them and given them refuge; they had been punished enough. I suggested this to General von Trotha, but he wanted their complete destruction."
Estorff's vision of a pacified and subjugated people integrated into the colonial system as a source of labor and livestock was harsh and destructive, but it was less extreme than the genocidal policy aggressively pursued by von Trotha with both the Herero and later the Nama. Estorff also felt his personal honor was at stake when he promised starving bands of Herero that they would not be harmed only to see them charged with murder and executed. During the war with the Nama, Estorff was so appalled by conditions in the Shark Island prison camp with its 90% death rate that he closed it down and moved the survivors inland.
Promoted to Oberstleutnant in 1906 and commandant of a 4,000 strong Schutztruppe in 1907, Estorff served in Southwest Africa until 1910 when he was succeeded as Schutztruppe commander by Joachim von Heydenbreck.
At the outset of World War I, now Major General Ludwig von Estorff lead an infantry Brigade with the 5th Army (Crown Prince) on the Western Front and was severely wounded at Dannevoux. The next year he commanded the new 103rd Infantry Division on the Eastern Front (his brother Maj. General Eggert von Estorff was killed in Russian that March). He was promoted to Lieutenant General in 1916 and later assumed command of the 42nd Infantry Division. He received his highest military decoration, the Pour le Mérite, in September, 1917.
Estorff was a Prussian aristocrat and a conservative military man, and it would be a mistake to make him out to have been either a defender of human rights or an ardent opponent of Hitler. In August, 1939 on Tannenburg Remembrance Day, he and many other veteran officers were given the brevet rank of General der Infanterie, which would not have been the case had he been out of favor with the Nazis at this time. It is not clear to what degree he actively worked against the Nazis in his last years of life.
*Die Kämpfe der deutschen Truppen in Südwestafrika bearbeitet von der kriegsgeschichtlichen Abteilung 1 des Großen Generalstabs Band 1: Die Kämpfe gegen die Hereros Berlin 1906)