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.

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Porewater and sediment biogeochemistry were studied in the Northeastern Mediterranean Sea. A series of redox reactions (oxic respiration, denitrification, iron reduction) take place in the Northeastern Mediterranean subseafloor. Diffusive nutrient fluxes contribute remarkable fraction to total nutrient budget in the study region.

ODTÜ Deniz Bilimleri Enstitüsü’nün son 40 yılda R/V Bilim-2 gemisi ile topladığı veriler Marmara Denizi’nin organik madde ve besin tuzları açısından giderek zenginleştiği ve oksijen azlığı (hipoksia) çekmeye başladığını göstermiştir. Marmara Denizi’nin iki tabakalı sistemini oluşturan üst 25-30 metredeki Karadeniz ve altındaki Akdeniz kaynaklı sular, oşinografide haloklin adı verilen keskin bir tuzluluk geçişi ile ayrılmıştır. Haloklin altı sularda özellikle Doğu Marmara›da ciddi hipoksia görülmekte ve artan azot ve fosfor tuzu girdileri ile Marmara Denizi aşırı üretkenlik- ötrofikasyon baskısı çekmektedir. 2021 yılındaki müsilaj patlamasının da temel nedeni Marmara Denizi’nin bu yeni biyojeokimyasal durumu sayılmalıdır. ODTÜ Deniz Bilimleri Enstitüsü koordinasyonunda T.C. Çevre ve Şehircilik Bakanlığı desteği ile yürütülen MARMOD projesi (2017-devam) ile Marmara besin bütçesinde en büyük payın sıra ile yayılı yükler, noktasal deşarjlar ve Karadeniz suyu olduğu sonucuna varılmıştır. MARMOD modelleme sonuçlarına göre karasal girdilerde en az yüzde 40’lık bir azot-fosfor yükü azalımı ile sistem hipoksia eşiğini en az 5-6 yılda aşabilir. Bir başka deyişle, son derece kırılgan bir ekosistem durumuna gelen Marmara Denizi için geriye dönüş mümkündür. Bu nedenle beklenmeden tüm kaynaklarda en güçlü efor ile yük azaltım önlemleri alınmalı ve denize ek besin yükü getirecek her türlü yeni uygulamadan kaçınılmalıdır.