Microcystin-LR (MC-LR) is prevalent in water and can be translocated into soil-crop ecosystem via irrigation, overflow (pollution accident), and cyanobacterial manure applications, threatening agricultural production and human health. However, the effects of various input pathways on the bioaccumulation and toxicity of MCs in terrestrial plants have been hardly reported so far. In the present study, pot experiments were performed to compare the bioaccumulation, toxicity, and health risk of MC-LR as well as its degradation in soils among various treatments with the same total amount of added MC-LR (150 μg/kg). The treatments included irrigation with polluted water (IPW), cultivation with polluted soil (CPS), and application of cyanobacterial manure (ACM). Three common leaf-vegetables in southern China were used in the pot experiments, including L., L., and L. All leaf vegetables could bioaccumulate MC-LR under the three treatments, with much higher MC-LR bioaccumulation, especially root bioconcentration observed in ACM treatment than IPW and CPS treatments. An opposite trend in MC-LR degradation in soils of these treatments indicated that ACM could limit MC-LR degradation in soils and thus promote its bioaccumulation in the vegetables. MC-LR bioaccumulation could cause toxicity to the vegetables, with the highest toxic effects observed in ACM treatment. Similarly, bioaccumulation of MC-LR in the edible parts of the leaf-vegetables posed 1.1~4.8 fold higher human health risks in ACM treatment than in IPW and CPS treatments. The findings of this study highlighted a great concern on applications of cyanobacterial manure.