This study quantified emission factors of black carbon (BC) and nitrogen oxides (NO x ) from 21 engines on in-use excursion vessels and ferries operating in California’s San Francisco Bay, including EPA uncertified and Tier 1–4 engines and across engine operating modes. On average, ∼60 fuel-based emission factors per engine were measured using a novel combination of exhaust plume capture combined with GPS location and speed data that can be more readily deployed than common portable emissions measurement systems. BC and NO x emission factors (g kg–1) were lowest and least variable during fast cruising and highest during maneuvering and docked operation. Selective catalytic reduction (SCR) reduced NO x emissions by ∼80% when functional. However, elevated NO x emissions that exceeded corresponding exhaust standards were measured on most Tier 3 and Tier 4 engines sampled, which can be attributed to inactive SCR during frequent low engine load operation. In contrast, BC emissions exceeded the PM emission standard for only one engine, and SCR systems employed as a NO x reduction technology also reduced emitted BC. Using these measured emission factors to compare commuting options, we show that the CO2-equivalent emissions per passenger-kilometer are comparable when commuting by car and ferry, but BC and NO x emissions can be several to more than ten times larger when commuting by ferry.