I am not qualified to give legal advise on this matter, but from my understanding this is what I know.
If your pond or lake discharges into state or federal waters then you will need a NPDES permit for applying pesticides.
Hmmm... unless there has been a significant change, as someone that tries to keep on top of this kind of thing (I'm a fish farmer and president of my state aquaculture association), I'm not aware of anything as far as NPDES permits for recreational pond owners unless your individual state comes up with something, or you have been deemed a "significant contributor of pollution" whereas the EPA will mandate you apply for an NPDES permit.
Last I knew NPDES permits only applied to aquaculture facilites that fell under the definition of a
CAAP (Concentrated Animal Aquatic Production) that
produces at least 100,000 pounds of warmwater fish per year, 20,000 pounds of coldwater fish per year, AND discharges continously 24/7 for 30 days or more. Furthermore you'd have to feed more than 5000 pounds of feed per calendar month to be classified as a CAAP. Obviously a recreational pond owner does NOT apply under this definition.
I discharge overflow 24/7 7 months of the year from a secondary pond from my trout pond and DO NOT fall under the definition of a CAAP as I only feed a couple hundred pounds of feed per month and produce only 500 lbs. of trout upon final harvest.
I'm also considered a "minor" water user as I pump under the 70 gpm that defines a "major" water user here in Indiana, so I do not have to apply for a permit there either. However this is my DNR Division of Water, so this probably varies from state to state.
I've had people whine about my pumping but there is nothing they can do about it, nor do I have any significant effect on my aquifer.