The border regions between Shenzhen and Hong Kong have been the most noted areas since the Shenzhen Special Economic Zone was developed in 1980. On the north part of the transborder, rapid economic development has been carried out during the recent years with its great achievements. Meanwhile, the rapid urbanization and the improper land use have also resulted in some environmental problems because of the loss of water and soil and the subsequent sediment transport. The apparent increase in sedimentation rate coincides with a rapid development within the Shenzhen river catchment. Relationship between the characteristics of economic development under the special process in the study area and those of sediment transport under the process of erosion, transport and sedimentation are discussed. As results, environmental impact on the sensative ecosystem within the Shenzhen H.K. border regions due to sediments are evaluated. According to the recent investigations, the serious deterioration of the ecological system resulted from the loss of soil and water appears mostly around the Buji river and in the newly developed areas in Baoan and Longgang District, which requirs the urgent countermeasures to control further erosion and conserve the natural system. As the contrast, the influence of the increase of the sediment deposition and water pollution in the ecological sensitive areas near the river mouth in the Deep Bay is still environmentally acceptable. However, in the view of the development plans in both Shenzhen and Hong Kong sides within the transboundary band in the near future, pre protection measures must be carried out to decrease the potential environmental impact which will possibly place restriction on the equitable economic development in the process of the “second economic revolution” in the area. To ensure the sustainable development in the area, some measures must be implemented, and the sediment related problems must be taken into consideration in various kinds of regional plannings such as water and soil conservation planning in the fluvial system, non point source pollution control planning, water project construction planning and other plannings.