Rivers have many service functions, and play an important role in people's living and agricultural production. During the last decades, intensive human activities have been threatening river ecosystem. For shipping, hydraulic engineering facilities (e.g. spur dikes) have been built along river bank to increase water depth. However, natural habitat conditions (i.e. substrate, flow regime, water physico-chemical properties) are accordingly altered. Therefore, it is necessary to select representative organisms as indicators to assess the aquatic ecological status of different habitat conditions, furthermore, management strategies are to be put forward. Macroinvertebrates are often considered as good indicators of long-term changes in environments due to their confinement to the bottom, long life cycles and limited abilities of movement. In this study, field investigations of macroinvertebrates in the West River were conducted in November 2009 (at low water level) and May 2010 (at high water level). Altogether 70 taxa of macroinvertebrates belonging to 30 families and 59 genera were identified. Among them were 16 annelids, 21 mollusks, 32 arthropods and 1 miscellaneous animal. The average density and biomass of total macroinvertebrates were 140 ind m−2 and 0.23 g dry weight m−2, respectively. Canonical Correspondence Analysis (CCA) revealed that major factors structuring macroinvertebrate assemblages were flow velocity (U), water depth (Z), conductivity (Cond), total nitrogen (TN) and substrates (clay, silt, cobbles and bedrock). Density and diversity of macroinvertebrates peaked in the cobbles, while biomass reached the maximum in the bedrock. It is indicated that stable and heterogeneous habitats were beneficial to development of benthic assemblages. To conserve these habitats, type and construction position of spur dikes should receive enough attentions. Thus, it is suggested that as few spur dikes as possible can be constructed in the riverbed covered with cobbles and bedrocks. Otherwise, the angle between spur dike and river bank need be analyzed to generate the appropriate flow regime which can prevent the stable substrates from being buried by sands. Some advice about length and separation distance of spur dikes is also presented.