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Coastal upwelling event can be observed clearly from drastic changes of seawater temperature and chlorophyll-a before and during the event. From observation and model output, time-series data of these variables provide important datasets to be used for further analysis, such as developing gaussian empirical model of net marine primary productivity (NPP). Here, the objectives of this study are to analysis variation of temperature and chlorophyll-a (chl-a) from both observation and model output datasets, and to evaluate model temperature and chl-a for estimating the NPP prior to and during the upwelling event in Bali Strait. The archive CTD collected in April, June and August 2013 and model output datasets were used in this study. It is shown that during peak of upwelling event in August 2013, observed temperature is minimum and chl-a is maximum in the upper 50 m depth. It is found surfacing isotherm of 25-26°C from sub-surface to sea surface. Furthermore, model output of temperature was in good agreement with observed data, complementing the evolution of upwelling for entire year. Estimated NPP from empirical model suggested that a high NPP distribution occurred in the eastern part of Bali Strait during peak of upwelling event.