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Diesel-fueled marine engines can contribute to both air and water pollution, particularly when cooling water is contacted with products of combustion in the exhaust system. Soy-derived compression ignition fuel offers a route to reducing these emissions and their effects. A 1972 Westerbeke marine diesel engine was mounted on a dynamometer and the exhaust was arranged so that sampling was possible both with (wet also termed scrubbing) and without (dry) water contact in the exhaust stream. Emissions testing was conducted using the steady state ISO E4 marine duty cycle. The engine was tested with 0, 10, 20, 50, and 100% methyl soy-ester blends with #2 off-road diesel. The pure alternative fuel offered a 45% reduction in particulate matter for both dry and wet tests, with carbon monoxide decreasing and oxides of nitrogen increasing slightly. Particulate matter (PM) reduction is significant in the water phase since it was noted that 40% of the PM entered the water phase upon wet testing. Fuel composition did not have a profound influence on the production of acetaldehyde, acetone, and formaldehyde in the exhaust. However, it was evident that wet testing, where the water contacted the cooling water, produced substantially lower formaldehyde and acetone, but substantially higher acetaldehyde than dry testing, where the exhaust was separated from the cooling water. Dry testing of marine diesel engines may therefore not truthfully reflect oxygenates produced in real use.