Microalgae are unicellular organisms that can be grown photoautotrophically and their abundance in natural valuable compounds makes their industrial cultivation attractive. Current technology only allows for cost-effective production of high-value compounds. Therefore, this thesis proposes the use of ecological theory and practice to improve the large-scale cultivation of low- to medium-value compounds in microalgae. In the first study a multivariate modelling approach determined the individual importance of several abiotic factors on the dynamics of a microcosm microbial community under oligotrophic and eutrophic conditions. The application of a simple model illustrated key causal relationships and demonstrated that nutrient enrichment significantly changed the relative importance of the tested abiotic variables to the dynamics of the microbial system. The second study utilised a metaproteomic approach to detail the mechanisms of co-existence and acclimation in the same microbial community. A decrease in microalgal exudation, in eutrophic conditions, affected bacterial acquisition of energy and nutrients. Furthermore, two microalgal-bacterial relationships, of potential use to synthetic ecology, were highlighted. Finally, in the third study, the competitive dynamics between two C. reinhardtii strains, a wild type and a high-lipid mutant, were studied utilising response surface methodology. In the co-culture with 25% wild type, intraspecific competition significantly increased triglyceride concentrations. The competition data also suggested there was little risk of the mutant displacing the wild type under any of the experimental treatments. Finally, the highest triglyceride productivity was found in the pure mutant culture, after just 24 hours, demonstrating potential to scale out a small batch biomanufacturing system. This thesis successfully coupled traditional ecology experiments with modern ‘omics techniques. Several existing hypotheses, regarding microalgal ecophysiology, were assessed based on their potential application in commercial microalgal cultivation. In sum, microalgal biotechnology can benefit from the integration of core principles of microalgal ecophysiology in the transition from laboratory to commercial-scale cultivation.