The Little Akaki River faces significant environmental challenges, including sedimentation, which may adversely affect biodiversity and aquatic ecosystems. Understanding the relationship between macroinvertebrate metrics and sediment index along this river is crucial for assessing the river ecological health. This study aims to evaluate the relationship between macroinvertebrate metrics and sediment index along the Little Akaki River. The research was conducted across seven sampling sites based on the accessibility, intended to use and biotope richness from April to May 2024, employing a multi-habitat sampling methodology. Macroinvertebrates were collected from gravel, sand, mud, vegetation, riffles and pools with a 500 µm D-frame net. A total of 5575 macroinvertebrates were collected from gravel, sand mud, vegetation, riffles, pools, sand and mud. With 11 orders and 32 families, 21 taxa were found at site 1 and the lowest number of taxa was recorded at site 7. Habitat quality had a positive correlation with percentage of Ephemeroptera, percentage of EOT, and Shannon diversity index (r =0.833, r = 0.880, and r = 0.939, respectively). PSI had positive correlation with number of taxa, and ASPT-ETHbios (r = 0.819, and r = 0.798, respectively). A plot of RDA analysis separated the macroinvertebrate taxa which showed significant correlation with HQI. Most sites were heavily sedimented. The study reveals a significant correlation between PSI, habitat quality index, and macroinvertebrate metrics, providing clear evidence that sedimented sites are also heavily polluted. The causal relationship between fine sediment and pollution indicators needs to be investigated in detail.