In the present study, a model of the lower-trophic pelagic food web of the Black Sea is considered in order to provide a quantitative understanding of the marked changes in the food web structure in response to changing top-down and bottom-up control mechanisms due to eutrophication, overfishing, and climatic changes. The simulations consider three particular parameters controlling the changes in the ecosystem structure due to these stressors; (i) the magnitude of the nitrate flux into the euphotic layer from the chemocline layer (enrichment due to eutrophication), (ii) the magnitude of predation control introduced by the planktivorous fish on mesozooplankton (fishery), (iii) the magnitude of the Q(10) parameter controlling temperature dependence of the Mnemiopsis growth (changing climatic conditions). A simulation assessing the level of enrichment on the ecosystem indicates a shift of the major trophic energy flow towards Noctiluca and Aurelia and thus showing how the ecosystem would degrade when a critical level of enrichment is passed. Increasing predation pressure of the planktivorous fish during the enrichment phase is shown to reduce the mesozooplankton biomass that in turn declines its predation pressure on Noctiluca population and thus allows Noctiluca biomass to increase, considering that mesozooplanton is assumed to feed on Noctiluca (at a level of 15% food preference) in the current model.. Noctiluca then acts as a major consumer and a critical element of the degraded food web structure. The overfishing of planktivorous fish stocks allows Mnemiopsis biomass to increase considerably under changing (warmer) climatic conditions at the end of 1980s, following a decade-long intense cooling phase. Thus, our results suggest that overfishing would not alone be able to promote a Mnemiopsis population outburst in the absence of warming.