It originates from Mount Ishikari in the Daisetsuzan Volcanic Group and flows through Asahikawa and Sapporo.

Lava from the volcanic Shikotsu mountains dammed the river and moved its mouth to the Ishikari Bay.

The name of the river is derived from the Ainu for "make(s) itself go round about something" (i-si-kari < kari meaning "(to be a) circle, round, loop; spin, turn, go around, go back and forth," si- "reflexive prefix, itself, oneself," and i- "it, something, an impersonal third person object marking prefix, middle voice inflection prefix), i.e. "winding (river)."

Extensive construction and cultivation projects over the centuries have shortened the Ishikari by approximately 100 kilometres, and have also led to the formation of numerous oxbow lakes (三日月湖, mikatsuki ko, lit.

The landscape and human activities along the Ishikari River, especially the hard life of tenant farmers, are described in the novel 'The Absentee Landlord' published in 1929 by the Japanese writer Takiji Kobayashi.