The river meanders from its western slopes near Crookwell, flowing south-east through Goulburn, turning north-east to near Bullio, flowing north-west to Barrallier, before finally heading north-easterly into its mouth at Lake Burragorang.

The Wollondilly River rises about 7 kilometres (4.3 mi) east of Crookwell and initially flows south, impounded by Pejar Dam, to a point near Pomeroy.

From here the Wollondilly River takes a wide detour to the north-west to Barrallier, where it turn east before eventually regaining its north-easterly course into Lake Burragorang.

[1] The subcatchment area is 2,699 square kilometres (1,042 sq mi), and the largest in the Hawkesbury–Nepean Catchment.

The name Wollondilly is said to be derived from wallandillii, an Aboriginal word for 'water trickling over rocks'.