In China, mechanical collection of cyanoblooms followed by soil-based treatments has been widely used as emergency strategies in many eutrophicated freshwaters. This study was to evaluate both efficiencies and potential risks of typical soil-based technologies. Results from this study indicated that over 90% of cyanobacterial biomass and 96% of dissolved microcystins (MCs) could be restrained in soils via three-level systems, which were much better than single-level systems. High concentrations of MCs, ranged from 65 to 276 ng g −1 and from 2.12 to 6.6 ng g −1 , were found in soils around treatment systems and croplands, respectively. In the soil solutions, MCs ranged from 0.35 to 2.0 μg L −1 , showing a potentially high leaching risk. In the samples from shallow groundwater near the treatment systems, MC concentrations were detected as high as 1.2 μg L −1 . Moreover, bioaccumulations of MCs varied between 22 and 365 μg kg −1 , and 19−222 μg kg −1 were found in 13 kinds of crops and 7 kinds of wild grass, respectively. Our results indicated for the first time that current soil-based technologies were effective but could pose potential environmental, ecological, and public health risks. Further improvements of these technologies were also proposed based on our findings.