Blooms of jellyfishes are perceived to have increased during the last decades causing interference with human activities of both recreational and professional type. Those blooms seem to hold correlation with human impacts and environmental changes such as overfishing, the increase of temperature, eutrophication or habitat modification. In this study we perform the first simultaneous analysis of population dynamics from three scyphozoan jellyfishes, Aurelia sp. (Linnaeus, 1758), Cotylorhiza tuberculata (Macri, 1778) and Rhizostoma pulmo (Macri, 1778). The effect of temperature, salinity, ichthyoplankton, nutrients and chlorophyll a concentration have been studied. These three species are present in the Mar Menor coastal lagoon where they show a spatial and temporal segregation of their populations and life cycles that allows them to reduce interspecific competition. Temperature and its seasonal cycle have been determined to be a key factor regulating the populations, triggering the stmbilation process either by an increase in temperature (C. tuberculata) or by a decrease in it (Aurelia sp.). Such segregation has a decisive effect on the ecosystem, since it allows a continuous temporal succession of top-down control on the lagoon trophic network.