Living organisms produce certain metabolites that can be toxic to other organisms. Biotoxins produced by microalgae and cyanobacteria have numerous adverse effects on the environment. Therefore, it is crucial to recognize and rule out biotoxins that could be present in different environments. Numerous techniques have been developed to detect biotoxins. Nanotechnology has improved precision and accuracy in the detection of biotoxins, and nanomaterials (NMs) have been employed in sensor configurations to boost their effectiveness. Furthermore, there has been a significant surge in investigation into the application of magnetic beads in biotoxin detection. Magnetic beads are implied to target pre-concentration, signal amplifiers, and the immobilization of toxins, which leads to sensitive, reliable, and robust analytical systems. Recently, microfluidic systems have been harnessed to detect these noxious agents due to their minimal sample and reagent consumption, automation and integration possibilities, and optimal range of portability. Hence, nanotechnology, along with microfluid systems can be ideal candidates to detect biogenic toxins in the environment. Therefore, this book chapter elaborates on the potential applications of nanomaterials, magnetic beads, and microfluidic systems for emerging environmental biotoxin detection.