Microcystin-LR (MC-LR), one of the most highly toxic microcystins, is widely present in aquatic ecosystems. This review first outlines the hazardous risks posed by MC-LR to the environment and human health, and then examines current detection methods and their limitations. To address these challenges, the article systematically discusses recent progress in nanomaterials-enabled biosensors for MC-LR detection. The review explores applications of novel nanomaterials in MC-LR biosensing, including quantum dots (QDs), graphene, MXenes, semiconductor metal oxides (SMOs), metal-organic frameworks (MOFs), covalent organic frameworks (COFs), metal nanomaterials, DNA nanostructures, and magnetic nanoparticles (MNPs). Through meticulous functionalization design, these nanomaterials significantly enhance the sensitivity and selectivity of diverse biosensors. Furthermore, the review examines various nanomaterials-enabled biosensing strategies, such as electrochemical, colorimetric, surface-enhanced Raman spectroscopy (SERS), fluorometric, and dual-mode detection. These strategies demonstrate high efficiency and sensitivity, enabling rapid and accurate detection while providing reliable technological support for real-time monitoring. The review highlights significant improvements in detection performance facilitated by nanomaterials and underscores their unique advantages and promising potential for MC-LR detection. By comparing the advantages and limitations of different nanomaterials and biosensing strategies, this work synthesizes recent advancements, current challenges, and valuable insights for future research. Given rapid progress in materials science and sensing technologies, nanomaterials-enabled biosensors hold significant promise for MC-LR detection. This review is expected to provide substantial support for environmental monitoring, food safety, and public health security.