Tom, a poor orphan, is employed by the villainous chimney-sweep, Grimes, to climb up inside flues to clear away the soot. While engaged in this dreadful task, he loses his way and emerges in the bedroom of Ellie, the young daughter of the house who mistakes him for a thief. He runs away, and, hot and bothered, he slips into a cooling stream, falls asleep, and becomes a Water Baby. In his new life, he meets all sorts of aquatic creatures, including an engaging old lobster, other water babies, and at last reaches St Branden's Isle where he encounters the fierce Mrs Bedonebyeasyoudid and the motherly Mrs Doasyouwouldbedoneby. After a long and arduous quest to the Other-end-of-Nowhere young Tom achieves his heart's desire.

In the four hundred and thirteenth year of the Christian Era, some three hundred miles above Alexandria, the young monk Philammon was sitting on the edge of a low range of inland cliffs, crested with drifting sand. Behind him the desert sandwaste stretched, lifeless, interminable, reflecting its lurid glare on the horizon of the cloudless vault of blue. At his feet the sand dripped and trickled, in yellow rivulets, from crack to crack and ledge to ledge, or whirled past him in tiny jets of yellow smoke, before the fitful summer airs. Here and there, upon the face of the cliffs which walled in the opposite side of the narrow glen below, were cavernous tombs, huge old quarries, with obelisks and half-cut pillars, standing as the workmen had left them centuries before; the sand was slipping down and piling up around them, their heads were frosted with the arid snow; everywhere was silence, desolation - the grave of a dead nation, in a dying land.