Upper Section (Headwaters near Sierra del Aguilar): The uppermost reaches of the Yacoraite are formed by the merging of the four source tributaries — Vicuñayoc, Casa Grande, San Carlos, and Casa Chica — high in the Sierra del Aguilar. This section is characterized by steep gradients, fast-moving water, and the rugged mountain terrain typical of the Cordillera Oriental. The high elevation of the source streams means cold, well-oxygenated water throughout much of the year.

Middle Section: As the river descends from the sierra, it transitions through a more moderate gradient, flowing through quebrada terrain with the characteristic narrow canyon passages locally known as "angostos." The western flank of the Quebrada de Humahuaca, where the Yacoraite flows, features gentler, more gradual slopes compared to the steeper eastern ridgelines, giving this section a somewhat more accessible character.

Lower Section (Boundary between Humahuaca and Tilcara): In its lower course, the Yacoraite forms the departmental boundary between Humahuaca and Tilcara before reaching its confluence with the Río Grande. This section may widen somewhat as it approaches the main valley floor, where the Quebrada de Humahuaca can reach floodplain widths exceeding 3 kilometers in places, though it can also narrow dramatically at canyon constrictions.