The macroinvertebrate community, physical–chemical water variables and hydromorphological indices were studied in the Turón River (Málaga, Southern Spain). Our study aims to improve the knowledge of the most influential environmental factors at different spatial and temporal scales in Mediterranean rivers, in order to establish better management of Mediterranean river ecosystems. To this end, in this work, seasonal sampling was carried out for one year to evaluate the effect of the characteristics of the drainage basin (i.e., geology, topography, land use) on the macroinvertebrate community. To this end, the environmental variables of the catchment basins were evaluated at three different scales: (i) watershed level, (ii) valley segment level and (iii) local level. The results showed that 13 environmental variables, 3 at the watershed scale, 5 at the valley segment scale and 5 at the local scale, influenced the macroinvertebrate community. Land use is the main explanatory variable at the watershed scale, while stream channel curvature is the most common variable at the valley segment scale, and the habitat assessment index is the variable with the strongest influence at the local scale. The influence of different spatial scales presented a seasonal variation. During spring, autumn and winter, the watershed scale exhibited the highest resolution (adjusted R2 = 0.20–0.29), while in summer, the local scale became the most significant in explaining the presence of macroinvertebrate taxa (adjusted R2 = 0.17). The obtained results emphasize the significance of temporal and spatial scales in Mediterranean rivers for adequate river ecosystem management.