There are several environmental and ecological effects of shipping. However, these are rarely assessed in total in the scientific literature. Thus, the aim of this study was to summarize the different impacts of water-based transport on aquatic and nearshore ecosystems and to identify knowledge gaps and areas for future research. The review identified several environmental and ecological consequences within the main impact categories of water discharges, physical impacts, and air emissions. However, although quantitative data on these consequences are generally scarce the shipping contribution to acidification by SOx- and NOx-emissions has been quantified to some extent. There are several knowledge gaps regarding the ecological consequences of, for example, the increasing amount of chemicals transported on water, the spread of non-indigenous species coupled with climate change, and physical impacts such as shipping noise and artificial light. The whole plethora of environmental consequences, as well as potential synergistic effects, should be seriously considered in transport planning.