Marine air pollution is a major contributor to seaports and coastal air pollution, and Israel has yet to seriously confront this issue. This study aimed to update previous marine air pollution estimations in Israel’s two major ports: Haifa and Ashdod. The objectives were to examine technical and regulatory measures to address the problem, to propose mitigation targets and to estimate their potential benefits. Based on a model of emission-calculations that relies on an updated ship-inventory data as well as real-time ships’ location and movement tools, the combined marine NOx, SOx and PM2.5 annual emissions in these ports were found to be 18,415, 15,128 and 1453 tons, respectively. These values are considerably higher than previous estimates, are comparable to the constant pollution emitted at ground level from a 1000-MW coal powered city power plant and are 3–20 times higher than the industrial and land transportation sectors in these cities. Relatively high nickel concentration in PM was found in Israel only relatively adjacent to the Haifa and Ashdod ports. Since high nickel concentration in PM is today mainly associated with marine air pollution, this finding supports the hypothesis that marine air pollution worsens the air quality in these cities. SOx and PM2.5 emissions can be reduced by 78% and 27%, respectively, if Israel enforces the revised International Convention for the Prevention of Pollution from Ships (MARPOL) Annex VI regulations in its territorial waters. While the latter step can achieve external benefits of NIS 518.4 million/year (EUR 132 million/year), additional mitigation actions and local regulations are suggested, focusing on NOx emissions but also on other pollutant criteria. Such actions can achieve further benefits of NIS 274.3 million/year (EUR 70 million/year). Achieving the suggested targets is challenging yet attainable, and their potential benefits will probably outweigh their costs.