This dissertation introduces three different topics on waterborne transportation. River transportation is a very important alternative for freight shipments in some countries. A significant portion of United States agricultural commodities transported via river barges. The lower portion of the Missouri River has been channelized to support barge traffic. Barge traffic has been used to move agricultural commodities to the Gulf of Mexico through Mississippi River to be exported overseas. Missouri River faced some weather issues such as drought in some years and flooding in others. Alternative transportation modes are important during the post-harvest period when the river has low-flow. The results showed a positive cost to agricultural freight in three years of a five years in dry period. In the other two years rail rates were estimated to be lower than barge rates. The second topic is using maritime distance to measure trade costs in agriculture. Maritime transportation holds an important position among other transportation means because it has some characteristics that others do not. Maritime shipping is critical to international trade because of the advantages that ships have by carry huge amounts of cargo for long distances. The impact of port-to-port maritime distance on US international trade to Europe and North and South America was tested. Unexpectedly result shows that trade increases with maritime distance. This impact decreases when the geographical distance is higher than the maritime distance. The third paper measures the efficiency and productivity of major Middle East container ports. Ports considered the main node to link the trading partners. The results indicate that eight ports out of 21 ports have low productivity.