Cyanobacterial toxins or cyanotoxins are a diverse group of compounds with differing chemistries; hence, a single analytical method can rarely be used to evaluate all potential compounds. Toxicity bioassays have been adapted to assess the toxicity of cyanobacterial samples. The most common of these assays is the Enzyme-Linked Immunosorbent Assay kit using antibodies raised to specific cyanotoxins. Testing with bioassays is expected to show whether the sample contains toxic substances and how toxic these substances may potentially be. Laboratory staff handling samples potentially containing toxic cyanobacteria and cyanobacterial toxins is potentially exposed to health hazards, and appropriate protective measures need to be implemented. Following a sampling trip, the samples arriving in the laboratory need to be processed further for analysis or storage. Three aspects are important for sample handling and storage: safety, sample processing to ensure stability and traceability.