Per code, you need at least one egress window in a basement and an egress window in any bedroom (a room with a door and closet). If you fill these windows, you are creating an issue that will certainly come up in the home inspection should you try to re-sell the home.

First the replacement windows weren't replaced very good and should of been air tight and water proofed from the start. Second I'd work on those drains.

If you have living space, those functions are required to have natural light and ventilation, unless you provide mechanical substitution, which you 99% chance don't have and won't have. Also, depending on what legal work was done to an existing basement and whether you have a bedroom, you may also need an emergency escape & rescue window.

What would be better is first investigate the window well drains to see if they are clogged and where they go (e.g. connect to footing drain tile or just a buried pipe) and the surface depth below window. Review your sump pump system. Then buy prefab or have some window well covers made which will block not only most rain, but snow and leaves.

sounds like the grading is not correct, the only water that come in should be directly from the sky.

Didn't think about the building code issue! Will reach out to our local planning/zoning dept to find out what the requirements are as far as windows in basement. The ground around the 3 windows is flat/level but there is a retaining wall behind the area with a raised pool (guessing this added to the amount of water that came into the wells). Does anyone know how to test the drains to see if they are working and draining properly?

All work done to refinish the basement was permitted and inspected as it progressed. No bedrooms but a large open living space and a finished bathroom and storage room.

It's possible the windows were not installed correctly. The old ones were hopper style windows and were replaced with double slider windows. We have window well covers on all but they are not water proof...any suggestions for window well covers that might keep water out?

"Does anyone know how to test the drains to see if they are working and draining properly?"

They would only be probably 3' or 4' long and straight, so pop off the drain cover and look in with a flashlight, drop a pebble down it, or stick a broom handle in it.

"any suggestions for window well covers that might keep water out?""

Any and every polycarbonate cover? Maybe some pictures would help, as something's not adding up.

Run water down the drain. Next rain go out and observe where the water is going. Even an unclogged drain can be problematic if it is pitched wrong or does not have a clear exit patch.

We had that happen and wasn’t the drain so much as the water table changed because the water level stayed constant. We put a drain in basement wall at the base of the well with a hose inside going to the sump pump. Worked great.

No window is meant to seal while completely submerged in water unless its in a submarine. For the time and money that you would spend closing up these windows, you are much better off fixing whatever is actually causing the issue. Grading, window well drainage, add covers, etc.

As mentioned above, the ventilation, natural light, and egress considerations could come into play if this lower level is legal living space of your home, although if its simply "finished basement" with typical 16x32 basement windows, that wouldn't be likely.

A friend with a below grade window had a sump pump installed for his window wells.

Took a few photos to show windows/wells/retaining wall location. When we had the rain fall it was 9" followed by another 9" so the wells were completely filled up as ground was so saturated there was no place for the water to go so the depth of water was above the well height. Windows looked like they were fish tanks similar to one posted above but water was all the way up to top. We were glad the glass didn't break but don't want to be caught in that situation again with the changing weather patterns! Retaining wall is about 25-30' from the window well which is to the far right behind the hydrangea.

18" is a 1000year rain that will probably occur every handful of years now. I don't imagine it was just the window wells, you probably had water coming in at the slab/wall joint but just couldn't see it. As long as the drains are free and clear, and your sump is working, then there's not much more with the wells you could do that are reasonable solutions.

You could, however, install some underground drainage to alleviate some of the massive amount of water coming down the hill, and your yard may look like it needs some swales to direct water away from, and around the house footprint anyway. I don't imagine it was strictly ground saturation leaching in the wells from below, you probably had standing water in the yard flowing over the top/side flanges. So the underground drainage would help minimize that, as long as there is somewhere lower elsewhere in the yard away from the house.