Forgive me If i am wrong, but aren't riparian rights private property? How could the state charge you for use of property?
You are right. These water rights are an extension of property rights. My guess is that these permit costs would be called some type of administrative cost.
EPA re-interpretated the Clean Water Act to allow for the regulation of run-off aka non-point pollution. It has been upheld by the courts. EPA sets the standards and each individual state sets the regs to acheive those standards.
Maryland's TMDL Program
Chesaepeake Bay Tributary Strategy