The source of the Iwaki River is at Mount Ganmori ()A in the Shirakami-Sanchi region, a mountainous, unspoiled expanse of virgin forest which spans both Akita and Aomori Prefectures. The river flows eastward as a small mountain stream, then joins several tributaries to form the scenic Meya Ravine. The multi-purpose Meya Dam is located in the upper reaches of the Iwaki River. The river turns sharply northward at the city of Hirosaki. The river crosses the broad Tsugaru Plain, where it is joined by the Aseishi, Hira, and To rivers before emptying into Lake Jūsan on the western coast of the Tsugaru Peninsula. The mouth of the Iwaki River at Lake Jūsan is known as Mitoguchi. Parts of the Iwaki River are protected as part of Towada-Hachimantai National Park, Tsugaru Quasi-National Park, and five prefectural parks. It flows through the following municipalities: Nishimeya, Hirosaki, Fujisaki, Itayanagi, Tsuruta, Tsugaru, Goshogawara, Nakadomari, and Shiura, where it enters Lake Jūsan.