It is essential to understand the patterning of biota and environmental influencing factors for proper rehabilitation and management at the river basin scale. The Hun-Tai River Basin was extensively sampled four times for macroinvertebrate community and environmental variables during one year. Self-Organizing Maps (SOMs) were used to reveal the aggregation patterns of the 355 samples. Three community types (i.e., clusters) were found (at the family level) based on the community composition, which showed a clearly gradient by combining them with the representative environmental variables: minimally impacted source area, intermediately anthropogenic impacted sites, and highly anthropogenic impacted downstream area, respectively. This gradient was corroborated by the decreasing trends in density and diversity of macroinvertebrates. Distance from source, total phosphorus and water temperature were identified as the most important variables that distinguished the delineated communities. In addition, the sampling season, substrate type, pH and the percentage of grassland were also identified as relevant variables. These results demonstrated that macroinvertebrates communities are structured in a hierarchical manner where geographic and water quality prevail over temporal (season) and habitat (substrate type) features at the basin scale. In addition, it implied that the local-scale environment variables affected macroinvertebrates under the longitudinal gradient of the geographical and anthropogenic pressure. More than one family was identified as the indicator for each type of community. Abundance contributed significantly for distinguishing the indicators, while Baetidae with higher density indicated minimally and intermediately impacted area and lower density indicated highly impacted area. Therefore, we suggested the use of abundance data in community patterning and classification, especially in the identification of the indicator taxa.