When the aged mathematician died at Mortlake in 1608 he left to survive him five or six out of his eight children. Michael, born at Prague, had died on his father's birthday in 1594. Theodore, born at Trebona, died at Manchester 1601. Arthur and Rowland were left. Katherine was his companion to the end. The three younger girls, Madinia, Frances and Margaret, had, for anything we know, survived the plague which was so fatal to their mother, but there is no trace of either of them after that event in March, 1606. Aubrey, indeed, did hear from Goody Faldo of a daughter, whose name he thinks was Sarah, married to a flax dresser of Bermondsey. Dee had no daughter Sarah, and Aubrey does not suggest a name for the problematic husband.

Arthur, the eldest son, we have followed through a childhood of accidents to his selection and setting apart with a solemn rite to be his father's "skryer" in the magic crystal, in the eighth year of his age. We have traced the failure of that ill-advised choice, and have seen the lad of thirteen sent off to Westminster School with a little trunk and his mother's blessing. The next events in his life recorded by his father are his being wounded by a foyne while fencing with Edward Arnold, and the grant of the chapter clerkship of Manchester, in 1600.

He married in 1602, lived for a while in Manchester, and began practising medicine. Wood says he spent some time at Oxford, but his name has so far not been found in any college admissions. In his will he is described as "Doctor of Physic." Probably he took his degree abroad. His marriage to Isabella Prestwich, daughter of a well-known Manchester justice of the peace, took place when he was twenty-two, and it is to be presumed that he continued living on in Manchester until his father left that city some time in 1605 or 1606, after the sad death of his wife. Arthur set up a practice in London some time about that year, although precise dates are not obtainable. He seems to have followed the common usage of hanging outside his door a list or "table" of medicines, and their excellent therapeutic properties, which were said to effect certain cures of several diseases. This attracted the attentio of the censors appointed by the Royal College of Physicians, who proceeded against him forthwith, under the powers granted them against empiricks, which they had exercised since the foundation of the College in the early years of Henry VIII. The learned members of the college esteemed this "crime" such an "intolerable cheat and imposture," that they summoned Arthur Dee to appear before them with his remedies that they might impose a due penalty upon his presumption. The rest of the story is unrelated, and we cannot say what fine or order was his reward.