The Lower Karori Reservoir (LKR) is a small, monomictic lake of 2.34 ha situated in the Karori Wildlife Sanctuary (KWS), Wellington. Over the past decade cyanobacterial blooms have become a common occurrence in this water body. In 2005 Anabaena planktonica was detected for the first time in the LKR and this species now forms dense blooms during summer. These blooms are problematic as they reduce aesthetic appeal and have resulted in odour problems for visitors to this high profile wildlife sanctuary. The objectives of this study were to identify key physical, chemical and biological variables influencing phytoplankton dynamics in the LKR and to use ecological models to investigate plausible management options. The key parameters investigated, that may cause bloom formation were; summer stratification, high nutrient levels, and the food web effects of a large population of European perch (Perca fluviatilis). High resolution sampling was carried out every six hours over a 72 hour period during pre-bloom, bloom and post-bloom periods in 2006/7 to elucidate short term temporal and spatial variations in biological and physico-chemical parameters. Quantitative polymerase chain reaction (QPCR) was used to enumerate A. planktonica populations, allowing a large number of samples to be simultaneously evaluated. Algal densities were also estimated using conventional phytoplankton enumeration and chlorophyll a analysis. Water samples were collected for nutrient analysis at discrete depths and profiles were taken for temperature, dissolved oxygen and photosynthetic active radiation. Secchi depth and pH were also measured. Weekly or fortnightly phytoplankton and zooplankton samples and physical variables have been collected at LKR since September 2005 as part of an independent sampling program carried out by the KWS, Waikato University and Cawthron Institute. In this project the 2-year data set was used to assist with analysis of lake processes and for validation of the hydrodynamic-ecological model DYRESM-CAEDYM. Between 12 and 15 February, 2007, electric fishing was undertaken within the LKR. A total of 3,946 P. fluviatilis were removed and the effects on phytoplankton and zooplankton concentrations were investigated. To increase knowledge of the physiology of A. planktonica, laboratory experiments were undertaken using cultures subjected to a range of different light intensities and temperature regimes The phytoplankton assemblage of the LKR shows very distinct temporal variations. Summer stratification occurred in the LKR for ~4 months each summer. During these periods A. planktonica comprised up to 99.9% of the surface phytoplankton population. During isothermy chlorophytes, bacillariophytes and small flagellated dinophytes are co-dominant in the phytoplankton assemblage. The results of the QPCR showed distinct diurnal vertical movement of A. planktonica, with the highest cell concentrations occurring at 1900 hours at the surface. Ammonium (NH4-N) is the dominant species of inorganic nitrogen during periods of stratification, while nitrate (NO3-N) is generally dominant during times of isothermy. Phosphate concentrations at surface and depth remained at low levels throughout the sampling period. The large surface populations of A. planktonica, are probably responsible for the elevated total nitrogen concentrations in surface waters during stratified periods. There appeared to be some short term effects of the P. fluviatilis removal with an increase in large crustaceans (e.g., Daphnia sp.) and a reduction in A. planktonica densities observed in the months following the P. fluviatilis removal. Only a small proportion of the total P. fluviatilis population was removed and it is unlikely that the effects will be long-lasting without subsequent removal steps. However, it seems likely that P. fluviatilis is one of the factors contributing to cyanobacterial blooms and management of this fish species should be considered in future lake restoration plans. Growth experiments indicated A. planktonica grow over a wide range of light intensities and temperatures, although highest growth rates were generally associated with higher temperatures (25 C) and light intensities (60 - 140 μmol m-2 s-1). Ecological and hydrodynamic trends within the LKR over a two year period were simulated with adequate success using the model DYRESM-CAEDYM. Management scenarios simulated using DYRESM-CAEDYM suggest implementation of an artificial destratification system in the LKR may be the most practical and effective means of controlling A. planktonica blooms. The addition of an artificial aeration system emitting air at a rate of approximately 50 l-1 s-1 should result in an isothermal system. Without summer stratification some of the physiological features of A. planktonica (e.g., buoyancy regulation and nitrogen-fixation) that give it a competitive advantage over other phytoplankton species will be reduced.