Its source is on the northern slope of Santa Rita Peak in the Diablo Range, 5.9 miles southeast of Idria within San Benito County.

Continuing toward the Fresno Slough to the northeast, but no longer reaching it, Cantua Creek ends shortly after passing under Interstate 5, 4 miles south of the census-designated place of Cantua Creek and just west of the California Aqueduct.

The Arroyo de Cantúa was first explored by a detachment of troops under José de Guadalupe Cantúa (1786–1860) who served in the Spanish army, stationed at San Juan Bautista, and lead the party that first explored the Arroyo Cantúa area while gathering in the Native American people that lived in the area for the Mission San Juan.

[4] The 19th century Spanish and Mexican El Camino Viejo trail crossed the Arroyo Cantúa in the San Joaquin Valley.

[2] The place was at Murrieta Spring 36°24′34″N 120°24′20″W / 36.40944°N 120.40556°W / 36.40944; -120.40556 a spring flowing from the south bank of the Cantúa forming a pool in the arroyo where it emerged from the foot of the western mountains, a mile above where California State Route 33 now crosses Cantua Creek.