Community ecology, often called synecology, is the study of interactions between species in communities at different geographical and temporal scales, including distribution, structure, abundance, demography, and interactions between coexisting populations. Investigating the effects of environmental, land use, and spatial factors on the composition of macroinvertebrate communities was the objective of the current study. From three watersheds in Ethiopia, we gathered 30 samples of environmental, land use, spatial, and biological components (macroinvertebrates). Variation partitioning studies were carried out to evaluate the unique and shared roles of environmental, land use, and spatial factors. We found that 51% of the variation in the compositions of macroinvertebrates could be attributed to environmental, land use, and spatial factors. Environmental characteristics were the most important component, accounting for 42% of the total variation explained. The key environmental variables that influenced changes in the composition of macroinvertebrate communities were pH, dissolved oxygen (DO), total organic nitrogen (TON), electrical conductivity (EC), temperature, and water depth. Land use and spatial factors also significantly contributed to the pattern of macroinvertebrate community composition, though they were less important than environmental influences. The study reveals that environmental factors are spatially structured and influenced by land use factors. Land use planning is a crucial strategy for improving stream conditions, increasing aquatic macroinvertebrate community composition, and enhancing freshwater ecosystem services.