In 1862 he assumed charge of the Coast Survey office, a position which during the war involved heavy responsibilities, which were soon aggravated by the beginning of the mental disease that incapacitated Mr. Bache for performance of the duties of Superintendent, and terminated in his death. Gradually Hilgard found himself forced to assume, one after another, the duties of Superintendent, until in the autumn of 1864 the whole devolved upon him, in addition to his duties as assistant in charge of the office. In this onerous and responsible position he remained, under heavy strain, until, in February, 1867, the appointment of Benjamin Peirce as Superintendent terminated the interregnum. All these extra services were rendered by him without compensation.