Surface phytoplankton productivity measurements were carried out in morphologically complex Lake Rotoiti with the objective of defining variations between sites and seasons, and the dominant environmental drivers of these variations. Measurements were carried out monthly at two depths at each of three morphologically diverse stations for 1 year throughout the lake. Productivity at the surface of the shallow embayment was significantly higher in most months of the year compared with the surface of the other two stations but there were no significant differences from September to December 2004. There were no relationships between measured environmental variables and primary productivity or specific production. Inorganic nutrient concentrations at the surface of the shallow station were low throughout the whole year but at the other two stations they showed a typical pattern for monomictic lakes of higher levels during winter mixing and declining concentrations during thermal stratification. The high variability between sites found in this study indicates that it is important to account for local differences in productivity in morphologically diverse lakes, and that whole lake productivity estimates may vary greatly depending on the location and depth of productivity measurements.