Abstract: In small-scale pumped-storage reservoirs, physical disturbances have been suggested to be one of the main factors influencing phytoplankton structure and water quality. This study presented data on dynamic changes of the phytoplankton structure and the quality of raw water sampled monthly from January 2011 to June 2012, in three locations (with two different water levels each) of a small pumped-storage reservoir of Macau main storage reservoir. The trophic state index, phytoplankton structure indices, and multivariate statistical techniques were applied for assessing trophic state, phytoplankton community, and spatio-temporal variations of the reservoir, respectively. The results showed that the reservoir was categorized as a eutrophic–hypereutrophic reservoir, with the dominance of Cyanophyta in 2011, and of Chlorophyta and Bacillariophyta in 2012. Lowest diversity/evenness and highest dominance happened in June 2011, while highest diversity/evenness and lowest dominance occurred in May 2012. Principle component analysis identified four factors that can explain 80.8% of the total variance of the water quality data, and cluster analysis generated two clusters of spatial similarity among the six sampling points and two clusters of temporal similarity among the 18 months. Discriminant analysis results revealed only three parameters (TP, NO-N, and Chl-a) that could afford 100% correct assignation in temporal analysis, while no spatial variation was found in spatial analysis. This study highlighted the usefulness of combination of these methods for the evaluation and interpretation of complex water quality data-sets and assessment of pollution level of small-scale eutrophic reservoirs. The results from the study can be used in developing monitoring program of freshwater bodies.