Anthropic activity affects the hydrogeomorphological quality of fluvial systems. River and valley classifications are fundamental preliminary steps in determining their ecological status, and their prioritization is essential for the proper planning and management of soil and water resources. Given the importance of the High Andean livestock micro-watershed (HAL-MWs) ecosystems in Peru, an integrated methodological framework is presented for morphometric prioritization that uses a Principal Component Analysis (PCA) and Weighted Sum Approach (WSA), geomorphological fluvial classifications (channel, slope, and valley), and hydrogeomorphological evaluations using the Hydrogeomorphological Index (IHG). Of six HALMWs studied in Leimebamba and Molinopampa (Amazonas region), the PCWSA hybrid model identified the San Antonio HAL-MW as a top priority, needing the rapid adoption of appropriate conservation practices. Thirty-nine types of river course were identified, by combining 13 types of valley and 11 types of riverbed. The total assessment of the IHG indicated that 7.6% (21.8 km), 14.5% (41.6 km), 27.9% (80.0 km), and 50.0% (143.2 km) of the basin lengths have "Poor", "Moderate", "Good", and "Very good" quality rankings, respectively. The increase in the artificial use of river channels and flood plains is closely linked to the decrease in hydrogeomorphological quality.