Estimates of the sources and wet deposition fluxes of inorganic nutrients (PO₄³⁻, NO₃⁻, NO₂⁻, NH₄⁺) have been made using a long‐term wet atmospheric deposition measurement at three sites along the Mediterranean coast of Israel. The nutrient composition in rainwater indicated a dominant anthropogenic source for NO₃⁻ and NH₄⁺ and a continental, natural, and anthropogenic, rock/soil source for PO₄³⁻. The calculated long‐term dissolved inorganic N (IN) and inorganic P (IP) fluxes were 0.28 and 0.009 g m⁻² yr⁻¹ to the coastal zone and estimated as 0.24 and 0.008 g m⁻² yr⁻¹ to the Southeast (SE) Mediterranean, with a possible increasing pattern of the annual dissolved IN fluxes. Concentration of total and seawater leachable IP (LIP) from dust was examined on 20 Whatman 41 filters collected during 1996. The mean total IP concentration in dust was 0.13 ± 0.11% (geomean = 0.09%), with a mean of 387 ± 205 μg IP per g of dust leached by seawater. LIP from dust varies between 6 and 85% (mean of 38%) of the dry total IP. Dust of desert‐type (Saharan) events exhibited lower LIP solubility in seawater (∼25%, median) than air masses of European origin (∼45%, median). The calculated ratio of wet deposition to total (wet and dry) deposition here of 0.2 showed the importance of dry deposition of P in the SE Mediterranean basin compared to atmospheric inputs into the northwestern basin. The total IP and seawater LIP fluxes from dry deposition were estimated as 0.04 and 0.01 g m⁻² yr⁻¹, respectively. Atmospheric inputs of bioavailable N and P represent an imbalanced contribution to the new production of 8–20 and 4–11%, respectively, and reinforce the unusual N:P ratios (∼27) and possible P limitation in the SE Mediterranean.