Veliko Jezero (“Big Lake”) is a semi-enclosed marine lake formed in a submerged karstic valley in a Croatian marine protected area, the Island of Mljet. Over the second half of the 20 century, the Veliko Jezero ecosystem undergone human-induced modifications related to the water mass exchanges with the open sea, which consisted in a 2-fold increase of depth in the channel communicating the lake with open sea. In this work we examine historical and recent data on hydrology and zooplankton abundance and structure that cover the period 1950-2001. Both, temperature and salinity showed upward trends and a maximum of 2°C in temperature, while salinity rose from 35.84±1.19, observed in the 1950s, to 37.43±0.56 recorded in late 1990s. Such changes have modified the pelagic habitat and altered the zooplankton structure through invasive processes and local extinctions. In particular, an increasing number of open-sea species, i.e. copepods and appendicularians, become more frequent and abundant, and former dominant species, i.e. the copepod Pseudocalanus elongatus, have disappeared since the 1990s. Concurrent to these changes, the biomass of jellyfish has increased, with the schyphomedusan Aurelia sp. 5 as the dominant species reaching abundances nowhere observed. These long-term modifications are discussed in regards to resilience and compensatory responses of zooplankton community to disturbance in a changing environment.