Over the last few decades, anthropogenic eutrophication has become a significant problem in New Zealand and other parts of the world. Lake Rotorua is located in the central North Island, New Zealand. It is a lake with significant historical, cultural and recreational values that has undergone anthropogenic eutrophication. Lake Rotorua has been exposed to anthropogenic impacts through conversion of forested land to agricultural use within its catchment, and the discharge of domestic sewage into the lake. Cyanobacterial blooms have become a common occurrence in the lake each summer. These blooms not only reduce aesthetic appeal but also have potential to affect human health. Lake stratification and physical mixing events are the most important factors influencing nutrient availability and phytoplankton growth in Lake Rotorua. The main objective of this study was to use high frequency monitoring data to investigate the significance of lake stratification events and how these events interact with the development of the cyanobacteria population and changes in nutrient concentrations in Lake Rotorua. The second objective was to use an ecological model to understand the relationship between physical, chemical and biological variables, and phytoplankton dynamics. Data from a high frequency real-time water quality monitoring buoy was used as the basis for 12 sampling trips to Lake Rotorua timed around stratification and mixing events. Water samples were collected from five different sites for nutrient analysis, chlorophyll a analysis, and phytoplankton and zooplankton identification at depth intervals of 6 meters. Profiles were taken for temperature, dissolved oxygen and fluorescence. Total suspended solids and volatile suspended solids were also analysed. The data provided by the buoy, combined with additional sampling and measurements around stratification events, were used to calibrate a three-dimensional ecosystem model, ELCOM-CAEDYM. Periods consisting of a few days of high solar radiation and low winds caused Lake Rotorua to become stratified between 26 January 2009 and 20 February 2009. During this stratification period the bottom waters became deoxygenated and there were large increases in of phosphorus and nitrogen concentrations in bottom waters, which were subsequently dispersed through the water column when the lake mixed again. Ammonium and phosphate were the dominant species of inorganic nitrogen and phosphorus in bottom waters during the periods of stratification. Upon mixing there was rapid growth of cyanobacteria (Microcystis sp. and Anabaena sp.). For the zooplankton community, copepod and rotifer densities increased significantly after the stratification event and replaced the previously dominant cladocerans. In the study high frequency modelling with ELCOM-CADYM simulated the general trends of water temperature, dissolved oxygen and nutrient concentrations in Lake Rotorua. The model captured the water temperature fluctuation before, during, and after lake stratification as well as subsequent dissolved oxygen changes over time and space. Simulated nutrient concentrations were close to the field measurements, in particular NH4, TN and TP. Some issues occurred with high frequency simulations such as being unable to capture the strong fluctuations of lake surface temperature, and the magnitude of the decreases in dissolved oxygen under strong stratification.