I see no mention of a standard for salinity. Tidal creeks on the seaside of Virginia's Eastern Shore have suffered reduced flushing action as the result of the headwaters of many of the creeks having been dammed, either by the construction of agricultural ponds or by the construction of Route 13. The creek on which I live (Kings Creek in Northampton County) suffers from both causes. As a result, there is minimal flushing of the creek, leading to increased levels of fecal coliform bacteria, decreased levels of salinity - as the salt wedge cannot move upstrean on high tides, and decreased numbers of oysters and clams growing in areas in which they were formerly plentiful.   

The upper portions of Kings Creek and many others are very shallow, not at all channelized, and do not flush properly. This leads to reduced numbers of fish and shellfish. Since shellfish are lacking, the water is no longer filtered effectively, leading to increased levels of fecal coliforms, and algal blooms. Crashing of the algal blooms can exacerbate low DO levels.

Every creek leading to the Chesapeake Bay in Northampton County has shellfish closures, due to high levels of fecal coliform bacteria, because of this poor flushing. 

The only solution I see ot this problem is instituting a salinity standard, removing the dams which cut off the headwater flows and dredging the creeks to restore the channels and flushing of the upper portion of the creeks.