The environmental friendliness of short sea shipping has been justified in Europe by the ensuing lower congestion at hinterlands and unneeded large-scale infrastructure investments on roads and railways. However, the attractiveness of short sea shipping is about to change. This is because of increasing environmental regulations (International Maritime Organization (IMO) sulfur regulation in the Baltic Sea and planned CO2 emissions trading) and increased world market oil prices. In this research, we analyze this potential change using data envelopment analysis on the existing transportation chain alternatives in the Helsinki (Finland) - Tallinn (Estonia) short sea route (chains using either roro, ropax or container ships). The analysis also includes the planned railway tunnel between the two cities. On the basis of our findings, the current truck and semi-trailer-based transportation is challenged by containers, irrespective of how they are carried (ship type). In the long term, for reasons of emissions and oil independency, the possibility of tunnel construction would make it vital to have container ship operations available along this route. The forthcoming change is not radical, but rather evolutionary and long term oriented.