Metabolites produced by microalgae profoundly affect the natural environment as the dominant organic carbon source in the ocean and the dominant organic sulfur source to the atmosphere. Of particular interest to this dissertation is the production of algal metabolites in response to changes in organism health and biological community turnover. In this dissertation, algal metabolites are investigated in highly complex marine and in controlled commercial-oriented environments. Measurements of organosulfur gases dimethyl sulfide, methanethiol, and dimethyl disulfide during marine mesocosm experiments show that the production of highly reactive non-dimethyl sulfide organosulfur compounds can comprise a far larger fraction of total sulfur released from the ocean than previously understood. This production was found to depend on the bacterial assemblages present in each mesocosm in combination with the biochemistry of the water. To more accurately measure algal metabolites in the natural environment, a new ionization method for high resolution mass spectrometry of high-salt organic samples was applied to analysis of marine samples. This method demonstrated the ability to analyze unprocessed seawater for the first time. To produce systems which replicate the turnover of natural marine algae, a review of the ocean-atmosphere simulator approach is given. As an exemplar of this approach, an intensive experiment utilizing an ocean atmosphere simulator is given which discusses the system performance and mesocosm characteristics. As microalgae are increasingly used commercially as a source of renewable biomass, understanding the production of metabolites in response to deleterious factors such as grazing is needed. The connection between algal grazing and production of grazing-specific metabolites was investigated by combining the results from imaging mass spectrometry, liquid chromatography mass spectrometry, and gas chromatography mass spectrometry. These studies found chlorophyll-a related breakdown products in the solid and liquid phases which were connected to measurements of volatile gases. Continuous measurements of volatile gases from microalgae by chemical ionization mass spectrometry were performed to understand the timescale in which gas production in response to grazing occurs. Chemical ionization mass spectrometry was found to be able to detect grazing in algal cultures 24-72 hours faster than current best methods, opening a new monitoring approach for commercial microalgae.