Microcystins are potent hepatotoxins produced by cyanobacteria, which proliferate in wastewaters with high nutrient content. Due to their high toxicity and potential risk to human health, even at low concentrations, the development of a sensitive and rapid method for the monitoring of microcystin‐LR (MC‐LR) in water samples is of great importance. In this context, a new direct electrochemical nano‐immunosensor for MC‐LR detection using the liquid crystal (E)‐1‐decyl‐4‐[(4‐decyloxyphenyl)diazenyl]pyridinium bromide (Br‐Py) as a redox probe and gold nanoparticles stabilized in bovine serum albumin (AuNP‐BSA) is described herein. The microcystin‐LR antibody (anti‐MC‐LR) was covalently immobilized using N‐(3‐dimethylaminopropyl)‐N‐ethylcarbodiimide hydrochloride (EDC) and N‐hydroxysuccinimide (NHS) on an AuNP‐BSA/BrPy film. The proposed sensor response is based on the inhibition of the Br‐Py electrochemical signal after the specific interaction of MC‐LR with immobilized anti‐MC‐LR on the electrode surface. The electrochemical behavior of the immunosensor was studied by square‐wave voltammetry (SWV) and electrochemical impedance spectroscopy (EIS). Under optimized conditions, using SWV and an incubation time of 15 min, the immunosensor exhibits a linear response to MC‐LR concentrations of 0.05 to 500.0 ng mL−1 with a detection limit of 0.05 ng mL−1. The anti‐MC‐LR/AuNP‐BSA/Br‐Py/GCE was successfully applied in the determination of MC‐LR in spiked seawater samples.