There is a high demand for developing accurate and sensitive microcystin-LR (MC-LR) analysis methods in complex environmental water due to its serious damage to human health. Herein, a self-assembled electroactive MOF–magnetic dispersible aptasensor has been developed to enable ultrasensitive MC-LR detection both in laboratory and in eutrophic water. Through the analyte-induced unwinding of an aptamer sequence-contained hairpin DNA on the surface of Zr-MOF electrochemical tag, the released chain-end can be easily found by the dispersible magnetic nanoparticles. Then the external magnet facilitated the aggregation of magnetic nanoparticles with captured MOF tags to the sensing surface. Thus, a highly sensitive self-assembled dispersible aptasensor for determination of MC-LR in environmental water samples without preconcentration was constructed. It was able to detect MC-LR from 0.005 to 100 ng mL−1, and was also employed successfully for MC-LR quantification in water samples from Lake Taihu, exhibiting a great potential for monitoring pollutants.