Aerosol and rainwater samples have been collected at a rural site located on the coastline of the Eastern Mediterranean, Erdemli, Turkey between January 1999 and December 2007. Riverine sampling was carried out at five Rivers (Ceyhan, Seyhan, Goksu, Berdan and Lamas) draining into the Northeastern Levantine Basin (NLB) between March 2002 and July 2007. Samples have been analyzed for macronutrients of phosphate, silicate, nitrate and ammonium (PO43-, Sidiss, NO3- and NH4+). Phosphate and silicate in aerosol and rainwater showed higher and larger variations during the transitional period when air flows predominantly originate from North Africa and Middle East/Arabian Peninsula. Deficiency of alkaline material have been found to be the main reason of the acidic rain events whilst high pH values (> 7) have been associated with high Sidiss concentrations due to sporadic dust events. In general, lowest nitrate and ammonium concentrations in aerosol and rainwater have been associated with air flow from the Mediterranean Sea. Comparison of atmospheric with riverine fluxes demonstrated that DIN and PO43- fluxes to NLB have been dominated by atmosphere (similar to 90% and similar to 60% respectively) whereas the input of Si was mainly derived from riverine runoff (similar to 90%). N/P ratios in the atmospheric deposition (233); riverine discharge (28) revealed that NLB receives excessive amounts of DIN and this unbalanced P and N inputs may provoke even more phosphorus deficiency. Observed molar Si/N ratio suggested Si limitation relative to nitrogen might cause a switch from diatom dominated communities to non-siliceous populations particularly at coastal NLB.