During this study, the effect of different processing methods on the microcystin quota (microcystins per cell) was investigated. Microcystins from two Microcystis strains and one Planktothrix strain were quantified using liquid chromatography-mass spectrometry (LC-MS) after processing via; (1) direct freezing (no prior cell concentration) and extraction by freeze-thaw cycles, (2) cell concentration by centrifugation and extraction in methanol and (3) cell concentration by filtration and extraction in methanol. Microcystin quotas were lower for samples concentrated by filtration compared with the other two methods. In order to distinguish between extracellular microcystins actively exported from cells and those that are present as a result of cell lysis, a comparative microcystin export (CME) assay was developed using LC-MS to compare the proportion of extracellular microcystins with the proportion of extracellular non-ribosomal peptide which does not get actively exported. A culture-based experiment using the CME assay demonstrated the utility of this method and indicated that export from one of the Microcystis strains had occurred. With further validation experiments, the CME assay has the potential to be a valuable new tool for determining the occurrence of microcystin export. An in situ experiment was carried out in Lake Rotorua, Kaikoura, New Zealand, using mesocosms to study the effect of Microcystis sp. cell density on microcystin production, while measuring a wide array of abiotic parameters (temperature, light intensity, pH, dissolved oxygen and nutrients). Lake water was added to ‘control’ mesocosms in which cells were concentrated to different levels and added to ‘medium cell addition’ and ‘high cell addition’ mesocosms. The microcystin quota remained relatively constant throughout the study, despite induced changes in cell density and associated environmental parameters. These results indicate that cell density is not the only factor responsible for increased microcystin synthesis and that further investigation into the effect of stress inducing abiotic parameters such as pH and dissolved oxygen concentration may be required.