The Eastern Mediterranean and its Cilician Basin offshore waters have oligotrophic features with low nutrient concentrations, low primary production, and high water transparency. However, the wide shelf area of the Cilician Basin is subject to contaminated river inflows with enhanced nutrient loads and direct discharges of urban wastewaters of southern Turkey, leading to develop local eutrophic/mesotrophic conditions in the inner sites of Mersin and Iskenderun Bays on the Cilician Basin. For the assessment of changing trophic status of the coastal and the bay water bodies under anthropogenic pressures since the 1980s, five extensive field studies were performed in summer and winter periods of 2014, 2015, and 2016. Physical and eutrophication-related biochemical parameters (salinity, temperature, Secchi Disk Depth, nutrients, dissolved oxygen, chlorophyll-a) were measured at 65 stations in different water bodies occupying the Northeastern (NE) Mediterranean coastal, offshore areas and bays. The collected data sets were used in scaling the trophic status of the visited water bodies of NE Mediterranean coastal, offshore areas and semi-enclosed bays, using novel classification tools of Trophic Index (TRIX), Eutrophication Index (E.I.), chl-a, and HELCOM Eutrophication Assessment Tool (HEAT), developed by different experts for highly productive seas. These tools, which can successfully classify highly productive coastal water masses under human pressures, and their sensitivities have been tested for scaling of the current trophic status of the NE Mediterranean coastal water bodies being subject to human pressures. The scaling results of classical TRIX, E.I., and chl-a indices in the NE Mediterranean water masses are not sensitive enough to differentiate mesotrophic and eutrophic water bodies because these indices principally assume to have higher concentrations of eutrophication-related parameters in the least effected (reference) water bodies. The HEAT tool, which uses a site-specific reference value for each eutrophication-indicator, has allowed us to produce more reliable and sensitive scaling of the current trophic status of the NE Mediterranean shelf areas, even though we used only the reference values derived from the composite data sets. The results of the indices were compared with the HEAT tool and the actual status was assessed from observations, indicating revision requirements of the multi-metric classification tools. For this goal, scales of natural (oligotrophic) and anthropogenic (eutrophic) levels of eutrophication indicators should be determined at a sub-basin scale using long-term site-specific observations in the NE Mediterranean. The revised scale ranges of TRIX for oligotrophic, mesotrophic, and eutrophic water bodies of Mersin Bay are in line with ranges of TRIX classification tool proposed for Aegean Sea waters, which can be used to assess trophic status of the entire Eastern Mediterranean and Aegean coastal seas (surface salinity >37.5) having oligotrophic properties in the offshore waters.