The construction of Fremantle harbour was probably O'Connor's greatest personal triumph, as his proposal to build the harbour within the entrance to the Swan River was contrary to previous expert advice that this was impracticable and that the construction would require constant dredging. Work commenced in 1892 in removing a limestone bar and sand shoals at the mouth of the Swan River and was successfully completed in 1903. On the 4th May 1897 the first overseas passenger vessel berthed alongside the wharf, which had been named Victoria Quay in honour of Queen Victoria, who celebrated her Diamond Jubilee that year. One hundred years of continued use of Fremantle Harbour by heavy shipping has vindicated O'Connor's technical judgement.
O'Connor is best known for his work on the Kalgoorlie Water Supply Scheme, also known as the Goldfields Pipeline. This pipeline carried and still carries water from Perth to the Goldfields. A succession of gold rushes in the Yilgarn region near Southern Cross, Australia in 1887, at Coolgardie in 1892, and at Kalgoorlie in 1893 caused a population explosion in the barren and dry desert centre of Western Australia. On 16th July 1896, John Forrest introduced to Western Australian Parliament a Bill to authorise the raising of a loan of £2.5 million to construct the Scheme: the pipeline would cart five million gallons of water per day to the Goldfields from a dam on the Helena River near Mundaring Weir in Perth, pumped in eight successive stages through 330 miles of 30 inch diameter pipe to a tank on Mt Burgess to the north of Coolgardie. The water is then reticulated to various mining centres in the Goldfields of which Coolgardie was one.
O'Connor was subjected to prolonged criticism by members of the Western Australian Parliament over the Scheme. He took his own life on 10 March 1902, less than a year before Forrest turned on the water from Mundaring Weir in Perth to Coolgardie and Kalgoorlie.
A bronze statue of C. Y. O'Connor by Pietro Porcelli stands in front of the Fremantle Port Authority buildings, commemorating O'Connor's achievements.