How to organize physical structure of media library/uploads folder

Hi! I am taking an existing website and putting it into WordPress, which means I already have a lot of content-100 or so pdfs, and 350 or more images. I would like to be able to organize these media files into folders by year when I create the site. However, because I am uploading all this content at one time, WordPress would like to stick it all in 1 folder and this creates a very unorganized, large folder. I’ve been looking at ways around this. Media taxonomy is nice, but I need the underlying file structure on the server to be changed. Any ideas on how I can accomplish this?

I’ve tried to put the content in separate folders, but WordPress seems to only recognize what is directly in the uploads folder, or in the subfolders that it created by default. Is there anyway I can tell WordPress to consider all of subfolders in “uploads”?

Thank you for any suggestions you can provide!