"Clongowes" refers to Clongowes Wood College, a boys' boarding school run by the Jesuits in Sallins, County Kildare. James Joyce was a student at Clongowes from 1888 to 1891 (ages 6-9), as was his fictional avatar Stephen Dedalus, whose life-defining experiences there are represented in A Portrait of the Artist as a Young Man. Joyce had to leave when his father could no longer afford the bills, and the same appears to be true of Stephen.
Many people at the time regarded Clongowes as the best Catholic school in Ireland, and a Jesuit education could be not only intellectually formidable but also socially advantageous. John Joyce took pride in the fact that his sons were educated so prestigiously. In A Portrait, Simon Dedalus refers contemptuously to the less distinguished Christian Brothers as “Paddy Stink and Micky Mud. No, let him stick to the jesuits in God’s name since he began with them. They’ll be of service to him in after years. Those are the fellows that can get you a position.” Stephen perhaps shares some of his father's pride in his education, but he also thinks ruefully of the gulf between his family (middle-middle-class and declining rapidly) and the upbringings that most of his classmates enjoyed. In Proteus he thinks of the lies he invented to save face: "You told the Clongowes gentry you had an uncle a judge and an uncle a general in the army. Come out of them, Stephen. Beauty is not there."
Experiences from his days at Clongowes continue to fill Stephen's mind. In Telemachus he remembers how "I carried the boat of incense then at Clongowes. I am another now and yet the same." In Proteus, as he imagines trying to save a drowning man, he thinks back to his reactions to the water basin at school. "Water cold soft. When I put my face into it in the basin at Clongowes. Can't see! Who's behind me? Out quickly, quickly!" Still another experience with cold water at Clongowes—being pushed into a cesspool by a sadistic classmate—lies behind his morbid fear of the element. In Ithaca Stephen remembers his time with "Brother Michael in the infirmary of the college of the Society of Jesus at Clongowes Wood," as he recovered from the alarming infection acquired in this incident.
In Wandering Rocks, Father John Conmee, who was the Rector of Clongowes during Stephen's time, recalls walking through the green fields that surround the school: "His thinsocked ankles were tickled by the stubble of Clongowes field. He walked there, reading in the evening, and heard the cries of the boys' lines at their play, young cries in the quiet evening. He was their rector: his reign was mild."