In order to meet stringent fuel sulfur limits, ships are increasingly utilizing new fuels or, alternatively, scrubbers to reduce sulfur emissions from the combustion of sulfur-rich heavy fuel oil. The effects of these methods on particle emissions are important, because particle emissions from shipping traffic are known to have both climatic and health effects. In this study, the effects of lower sulfur level liquid fuels, natural gas (NG), and exhaust scrubbers on particulate mass (PM) and nonvolatile particle number (PN greater than 23 nm) emissions were studied by measurements in laboratory tests and in use. The fuel change to lower sulfur level fuels or to NG and the use of scrubbers significantly decreased the PM emissions. However, this was not directly linked with nonvolatile PN emission reduction, which should be taken into consideration when discussing the health effects of emitted particles. The lowest PM and PN emissions were measured when utilizing NG as fuel, indicating that the use of NG could be one way to comply with up-coming regulations for inland waterway vessels. Low PN levels were associated with low elemental carbon. However, a simultaneously observed methane slip should be taken into consideration when evaluating the climatic impacts of NG-fueled engines.