Transformations of land use from natural to anthropic type have been recognized as a significant trigger which degenerate the aquatic ecological quality seriously. However, there was still lack of enough evidence which the extent of changes in land use should be set as a biodiversity conservation target to protect aquatic ecosystem. To understand the corresponding variations of aquatic organisms to environmental gradients and set the conservation threshold values for land use, data of physicochemical parameters and macroinvertebrate communities were sampled in the Hun-Tai River Basin during 2009 and 2010. The main objectives of the present study were (i) to explore limiting factors that affect the distribution of macroinvertebrate communities with land use gradients, (ii) to estimate thresholds for the conservation of macroinvertebrate communities derived from generalized additive models (GAMs) and Threshold Indicator Taxa ANalysis (TITAN), respectively. The results indicated that macroinvertebrate communities’ structure and integrity were strongly negative with nutrient, organic contaminants content, %CropArea and %ImperviousArea. Under a precaution perspective and given current levels of land use, this research might provide some useful strategies for appropriate land exploitation management and improving water quality and biodiversity conservation in river ecological restoration.