"[6] O'Shaughnessy was born to farmers Patrick and Margaret (née O'Donnell) at the family cottage named Jointer in Loughill Parish, County Limerick, Ireland on May 28, 1864;[7]: 1  he was one of nine children.

[8] At two years old, he was sent to live with his maternal grandparents, approximately 16 mi (26 km) east of his birthplace, along with his Uncle Maurice, Aunt Alice, sister Kate, and cousin Margaret O'Clery, who had been orphaned.

[7]: 2–4  In 1875, he entered the Mount Trenchard National School and completed his studies there on September 25, 1880,[7]: 33  whereupon he tried his hand at farming briefly before deciding to train as a civil engineer.

[7]: 45 [2][9] After returning to the family home for a few months, O'Shaughnessy visited London in January 1885 to sightsee and apply for a position, but was encouraged to pursue his career in California instead.

[7]: 78 None of the letters of introduction that O'Shaughnessy had carried from Ireland led to a job, but he remained active in the local Irish community, where he struck up a friendship with Dr. Buckley, who had graduated from Queen's College Cork and arranged for O'Shaughnessy to start as an assistant engineer for the Sierra Valley & Mohawk Railway in Plumas County, California in January 1886, at the salary of US$40 (equivalent to $1,400 in 2023) per month, with board included.

[7]: 52  After three or four months, O'Shaughnessy was dismissed; on the stage back to San Francisco, he received a letter from the Southern Pacific Railroad offering employment,[7]: 55–56  where he was responsible for laying out the towns of Niles, Tracy, Sanger, Lindsay, Porterville, Merced, Mill Valley, and Dinuba[3] between 1886 and 1888.

While O'Shaughnessy was looking for an easier route down the mountain, he found a brook just below the summit and refilled his jug, returning to refresh the party's spirits for the descent.

[7]: 100 [11] After arriving at Honolulu, he took a train to the Waianae Sugar Company plantation and hiked 6 mi (9.7 km) to visit water tunnels nearby, through which flowed 2,000,000 US gal/d (5,300 L/min).

[7]: 116  After returning to Kaunakakai, O'Shaughnessy sunk some test wells and discovered that at the proposed pumping rate, the irrigation water would become contaminated with salt, which proved true once the station began operating in May, causing the plantation on Molokai to founder and he was let go by the company.

[7]: 144–149 [3][14]: 401  His time in Hawaii was interrupted by the 1906 San Francisco earthquake and subsequent fire, which he learned of on April 18 during a trip to Honolulu to procure cement; O'Shaughnessy booked passage on the next available ship.

[7]: 157–159 In December 1906, O'Shaughnessy was contacted by the brothers John D. and Adolph B. Spreckels, who asked him to inspect the work in progress on Morena Dam, which they were building at Barrett near San Diego to supply water to the city, and estimate the cost and schedule to complete it.

O'Shaughnessy was hired by John Spreckels to act as a consulting engineer for the project in May 1907; a construction contract was let that July and water began flowing to the city's Lower Otay Reservoir via the Dulzura Conduit,[8] an aqueduct connected to Morena Dam, on January 3, 1909, six months ahead of schedule.

On December 28, the Spreckels brothers called O'Shaughnessy to their offices in San Francisco, where they presented him with a bonus check "in five figures to make up the deficit which they felt they owed me".

After taking over on September 1 from the retiring city engineer, Marsden Manson, O'Shaughnessy took action within a week to minimize costs and preserve schedule by denying a request to line the planned Stockton Street Tunnel with brick.

[7]: 84  With the completion of the Twin Peaks Tunnel, Market Street was equipped with four streetcar tracks and the business interests which previously had opposed its construction for fear it would hurt their profits found their sales doubling and quadrupling instead.

[22]: 5–8 The majority of O'Shaughnessy's time as city engineer was spent on the Hetch Hetchy project, which would bring water from the Tuolumne River and Yosemite Valley to San Francisco, a distance of 167 mi (269 km).

Funeral services were held at St. Vincent de Paul Church on October 15,[3] attended by San Francisco Mayor Angelo Rossi, and he was buried at Holy Cross.

[9] The Bancroft Library, University of California, Berkeley holds an archive with primary source material relating to O'Shaughnessy's job as City Engineer of SF.