An analysis of the induced changes in both total productivity and community structure as a consequence of different pulsed nutrient inputs has been made by using two different ecosystem modeling tools. One was a modified version of the N-based model proposed by Fasham et al. (1990) for pelagic ecosystems and the other the plankton functional type model by Vichi et al. (2007). Both models lead to higher total biomass production with a pulsed nutrient input compared to a continuous supply, affecting both phytoplankton and zooplankton. Detailed responses are, however, different among plankton groups depending on the frequency of pulsed nutrient input and the complexity of the model. The differences in biomass production were higher for an oscillation period of 150–170 days following a sinusoidal supply pattern. A tidal mixing-induced nutrient supply was also simulated by using both models and a larger biomass increment was observed compared to that obtained with the sinusoidal pattern. Finally, a theoretical application of this approach to the pelagic ecosystem of the North Western Alboran Sea shows a preferential selection of diatoms and larger zooplankton under discontinuous nutrient inputs.