This study assesses the ecological status of alpine lotic ecosystems in Khunjerab National Park, Pakistan, situated at approximately 4000 m in the Karakoram Range along the Pakistan–China border. An integrative approach was employed, evaluating alpine stream ecosystems through benthic macroinvertebrate indices in conjunction with physicochemical habitat parameters. Samples were gathered using kick nets and hand-picking at seventeen randomly selected sites in early spring and summer. The study recorded 710 summer taxa from 41 families and seven orders, and 1250 early spring taxa from 30 families and six orders. The abundance of macroinvertebrates increased in early spring, while taxonomic diversity increased during the summer. Statistical tests revealed a strong relationship between water quality conditions and biological features. The biotic index reached its peak in early spring, while diversity indices peaked in summer when Ephemeroptera dominated. Due to the macroinvertebrate source in early spring, the majority of EPT taxa were abundant at all alpine stream sites during early spring, except for upstream sites in summer. The indices from the biotic metric evaluation revealed low levels of natural environmental disturbance caused by humans. This research is significant in terms of natural resource conservation and health assessment based on the benthic fauna community structure in alpine streams.