High-mountain lakes are freshwater ecosystems situated above the tree line which are known for their remote locations and limited accessibility. These ecosystems host simplified biotic communities primarily concentrated in the littoral zone and dominated by benthic macroinvertebrates that serve as bioindicators of environmental pressures. A two-year monitoring investigation was performed in July 2022 and July 2023 at Nero Lake (Cesana Torinese, Northwest Italy). Five sites along the lakeshore were selected for sampling physicochemical water parameters and macrobenthos. All collected data were analysed to compare trends across years and within specific sites. The results revealed that Nero Lake exhibited consistent macrobenthic communities across the two years studied, but significant differences were observed in its microhabitats. This suggests that substrate type and physicochemical water parameters strongly influence community composition. Chironomidae larvae and Mollusca were the dominant species, showing distinct associations with different substrates and environmental factors from one year to another. These findings contribute to our understanding of the intricate relationships between benthic macroinvertebrates and their environments, highlighting the necessity of detailed, small-scale assessments to comprehend ecosystem dynamics and develop effective conservation strategies.