Spatial and temporal variability and bloom formation of the potentially toxic diatom Pseudo-nitzschia spp. was investigated weekly to monthly from October 2009 to October 2010 in a eutrophic estuary, the Golden Horn. Pseudo-nitzschia spp. were detected in 195 of 512 samples (38%) collected throughout the year. Two species, P. calliantha and P. pungens, were identified based on the SEM examination. Blooms of Pseudo-nitzschia occurred in the lower and middle estuary in January and May. The bloom in January mainly comprised P. calliantha. In the bloom in early May, P. calliantha made up 72% of the Pseudo-nitzschia cells and P. pungens 28%. However, the contribution of P. pungens increased to 83% in late May. The Pseudo-nitzschia blooms occurred at low temperature (9–15°C) and moderate salinity (17–18), and for P. calliantha a significant negative correlation was found with temperature and a significant positive correlation with salinity. The percentage of Pseudo-nitzschia cells decreased gradually from lower to upper estuary (59–14%), correlating with a decrease in Secchi depth (5.5–0.5 m). Principal components analyses (PCA) were used to explore the spatial and temporal variability of environmental factors in relation to Pseudo-nitzschia abundances, and showed that NH4, pH, Secchi depth and DO values were the most important factors reflecting spatial differences, while temperature, salinity, Chl-a and Si:N were more important factors showing temporal differences. High abundances of P. pungens correlated mainly with pH, Secchi depth and DO values, whereas P. calliantha also correlated with NO3 + NO2. Low light availability due to high concentrations of suspended material and very variable environmental conditions (e.g. pH, DO and NH4) may have limited growth of Pseudo-nitzschia in the upper estuary. Regular monitoring of Pseudo-nitzschia is important for improving the understanding of the influence of environmental parameters on bloom dynamics in the study area.