Emissions from harbor-craft significantly affect air quality in populated regions near ports and inland waterways. This research measured regulated and unregulated emissions from an in-use EPA Tier 2 marine propulsion engine on a ferry operating in a bay following standard methods. A special effort was made to monitor continuously both the total Particulate Mass (PM) mass emissions and the real-time Particle Size Distribution (PSD). The engine was operated following the loads in ISO 8178-4 E3 cycle for comparison with the certification standards and across biodiesel blends. Real-time measurements were also made during a typical cruise in the bay. Results showed the in-use nitrogen oxide (NOx) and PM(2.5) emission factors were within the not to exceed standard for Tier 2 marine engines. Comparing across fuels we observed the following: a) no statistically significant change in NO(x) emissions with biodiesel blends (B20, B50); b) ∼ 16% and ∼ 25% reduction of PM(2.5) mass emissions with B20 and B50 respectively; c) a larger organic carbon (OC) to elemental carbon (EC) ratio and organic mass (OM) to OC ratio with B50 compared to B20 and B0; d) a significant number of ultrafine nuclei and a smaller mass mean diameter with increasing blend-levels of biodiesel. The real-time monitoring of gaseous and particulate emissions during a typical cruise in the San Francisco Bay (in-use cycle) revealed important effects of ocean/bay currents on emissions: NO(x) and CO(2) increased 3-fold; PM(2.5) mass increased 6-fold; and ultrafine particles disappeared due to the effect of bay currents. This finding has implications on the use of certification values instead of actual in-use emission values when developing inventories. Emission factors for some volatile organic compounds (VOCs), carbonyls, and poly aromatic hydrocarbons (PAHs) are reported as supplemental data.