Cyanobacteria are an ancient group of photosynthetic prokaryotes that are found in a wide range of habitats including freshwater lakes and rivers. In aquatic ecosystems, under favourable environmental conditions, cyanobacteria can form dense and expansive blooms. The increasing prevalence of cyanobacterial blooms globally has been linked to environmental changes in freshwater ecosystems including anthropogenic eutrophication, catchment modification and climate change. One of the most common genera of bloom-forming cyanobacteria is Microcystis. It can produce microcystins, a potent cyanotoxin that poses a risk to human and animal health. It also possesses physiological adaptations that confer a competitive advantage over other phytoplankton and cyanobacteria. One of these is the ability to vegetatively ‘overwinter’ on sediment surfaces. When conditions are favourable in spring or summer cells are recruited back into the water column and may provide a substantial inoculum for summer blooms. To better understand the variables that promote Microcystis aeruginosa blooms, this study investigated; (i) how environmental variables influence M. aeruginosa bloom formation and species succession during a bloom, as well as the seasonal variability of microcystin production, and (ii) how environmental, biotic and ultrastructural changes in the cells influence recruitment of benthic M. aeruginosa. The study focused on Lake Rotorua, a small eutrophic lake in Kaikoura, South Island, New Zealand. To address the first objective, surface water samples were collected weekly or fortnightly from Lake Rotorua between 14 January 2014 and 27 May 2015. Samples were analysed for cyanobacterial cell density and species composition, total and dissolved nutrients, mcyE genotype composition, and microcystin quota. Temperature was measured using loggers at different depths in the water column and weather data were acquired from the Kaikoura weather station (approximately 8 km from the study site). To address the second objective, surface sediment samples were collected from near-edge (containing Microcystis and Aphanizomenon gracile) and mid-lake (containing predominantly Microcystis) sites in Lake Rotorua. A series of laboratory experiments were undertaken which investigated the effect of ammonium (0, 0.1, 0.2, 0.5, 1 and 5 mg N L-1), light intensity (dark, 1.5, 10, 50 and 100 µmol photon m-2 s-1) and temperature (4, 13, 16, 19 and 25°C) Changes in cellular structures of Microcystis isolated from sediment collected in spring, early and late summer were also analysed using transmission electron microscopy to assess how this influenced recruitment Cyanobacteria species composition in Lake Rotorua was dominated by Microcystis aeruginosa, Aphanizomenon gracile, and Dolichospermum crassum. Moderate levels of nitrate in the lake appeared to be related to intermittent high-rainfall events during the austral summer of 2014, and may have contributed towards dominance by A. gracile and D. crassum. While both species are capable of nitrogen-fixation, heterocytes were absent. M. aeruginosa blooms subsequently occurred when ammonium concentrations increased, water temperature was high (>27°C), and the total nitrogen: total phosphorus ratio was low. A storm towards the end of the 2014 summer rapidly cooled and mixed the lake, and was followed by bloom collapse. In contrast, an extended drought over summer 2015 resulted in prolonged stratification, increased dissolved reactive phosphorus and very low dissolved inorganic nitrogen concentrations. Cyanobacterial pattern of species succession differed substantially between 2014 and 2015. Aphanizomenon gracile and D. crassum contained a higher heterocytes frequency compared to 2014 and M. aeruginosa density remained relatively low. Picocyanobacteria consisting of Aphanocapsa sp. were abundant. There was no relationship between toxic genotype abundance and M. aeruginosa biovolume or environmental parameters. However, univariate analysis showed that there was a significant positive relationship (p<0.001) between microcystin quotas and surface water temperature. In all benthic recruitment experiments single cells, rather than colonies, accounted for the majority (>55%) of recruited cells and it was speculated this may have been because they had more immediate access to light and nutrients. Linear Mixed Effect Models (LMEMs) analysis showed that M. aeruginosa recruitment was significantly lower (ANOVA; p<0.001) in near-shore sediment samples, suggesting that A. gracile may elicit allopathic effects on M. aeruginosa. In mid-lake sediment samples, M. aeruginosa recruitment was significantly higher at moderate ammonium concentrations (0.1, 0.2 and 0.5 mg N L-1; ANOVA; p<0.001), at two temperatures (16 and 25°C; ANOVA; p<0.001) and high light intensities (50 and 100 µmol m-2 s-1; ANOVA; p<0.01). Under transmission electron microscopy the area of benthic cells occupied by gas vesicles increased significantly (ANOVA; p<0.001) for the three samples collected during the study period. The results highlight the complex successional interplay of cyanobacteria species and their physiological adaptations (e.g., nitrogen fixation, buoyancy regulation). Climate, through its effect on runoff, water temperature and stratification, can lead to successional sequences amongst different cyanobacteria species according to whether the combination of physiological adaptations is advantageous or disadvantageous with environmental change. The benthic recruitment experiments collectively demonstrated that allopathic interactions, ammonium, light and temperature individually and synergistically regulate gas vesicle synthesis and M. aeruginosa recruitment in Lake Rotorua.