It just means that the waterways are currently too narrow or too shallow for such increasingly massive ships, either naturally or because the deepening simply hasn't caught up to the increasing size of cargo vessels. The U.S. Army Corps of Engineers is involved with many port dredging projects to make the navigable waterways deeper and wider.[1] There has always been an iterative relationship between size/draft of ships and width/depth of waterways -- in fact, the size of many ships the world over is constrained for practical purposes by the size of the Panama Canal.[2]
The US government has been improving ports since its early days. In fact, the expenditure of federal funds on "internal improvements" such as port improvements was quite the contentious issue in the early republic.[3] But most of the world's trade moves by sea, and the US is and always has been a maritime nation.[4] The ROI for port improvements is laughably high, so it has always been a no-brainer.
[1] http://dqm.usace.army.mil/Education/Index.aspx
[2] http://en.wikipedia.org/wiki/Panamax
[3] http://en.wikipedia.org/wiki/Internal_improvements
[4] http://www.stratfor.com/analysis/geopolitics-united-states-p...