The influence of distinct tidal characteristics and nutrient status on mesozooplankton community was studied in six major estuaries along the west coast of India during the late-monsoon (MS) and post-monsoon (PM) periods. The macro-tidal estuaries in the north (Amba and Thane) exhibited higher nutrient concentration compared to the micro- and meso-tidal estuaries located in the south (Cochin and Nethravati) and central (Zuari and Mandovi) west coast of India. The markedly higher nitrate and phosphate levels in the macro-tidal estuaries during PM indicated anthropogenic contributions from domestic and industrial effluents, which significantly impacted the mesozooplankton community structure. Nutrient enrichments favored higher phytoplankton standing stock leading to low DO levels. In the micro- and meso-tidal estuaries, meso- and euryhaline copepods dominated whereas in the macro-tidal estuaries, the copepod community was dominated by euryhaline and coastal species. Furthermore, the high-saline eutrophic environment of macro-tidal estuaries formed congenial for the increased jellyfish preponderance during PM. The predation pressure exerted by the jellyfish population on the crustacean zooplankton and ichthyoplankton exerted an adverse impact on the potential fishery stock in the macro-tidal estuaries. Thus, the study reveals that the nutrient enrichment favoring a shift in the mesozooplankton community structure from nutritionally superior crustacean plankton to less desirable jellyfishes, which in turn, may lead to a threat on the estuarine pelagic energy transfer and ecosystem deliverables.