I hate to be the bearer of bad news, but there is a pretty good chance that your project area is defined as a "wetland".

If so, then you may need permission at the federal level from the Corps of Engineers to modify the wetland in any fashion.

Converting a wetland into a pond MIGHT be permitted if it is considered an improvement. They frequently do not consider that an improvement.

I do not know the rules for New York, but I am pretty sure they also have state rules about converting wetlands.

You need to get your permits approved (or be granted exceptions in writing) before you make any modifications. The potential fines are BIG!

Hopefully, you can get an expert response from a member in NY that has completed a similar project.

Good luck on your pond!

(But I am worried that the paperwork and permits may scuttle your project.)