Microcystin-LR is a potent hepatotoxin produced by certain strains of cyanobacteria, commonly found in freshwater ecosystems during algal blooms. Its primary significance lies in environmental and public health monitoring due to its high toxicity when ingested through contaminated water or food. It is a key indicator in water quality testing, especially in reservoirs, lakes, and drinking water supplies prone to cyanobacterial blooms.

Due to its ability to inhibit protein phosphatases 1 and 2A, microcystin-LR is used in laboratory research to study cellular signaling pathways, particularly those involving phosphorylation and its role in apoptosis, cell cycle regulation, and liver toxicity. This makes it a valuable, though hazardous, tool in toxicology and molecular biology studies.

Because of its stability and toxicity, regulatory agencies use microcystin-LR as a reference compound to develop detection methods, such as ELISA, PCR, and mass spectrometry, aimed at identifying cyanotoxins in environmental samples. It also plays a role in evaluating the efficiency of water treatment processes like oxidation, filtration, and activated carbon in removing cyanotoxins.

Long-term exposure, even at low levels, is linked to liver damage and has been associated with increased risk of liver cancer, making it a focus in epidemiological studies and risk assessment for drinking water safety.