OK, let's back up a little:
1. Problem: It appears from your picture that you are pumping water from this hole without accessing it? So the cover you're looking for is to keep critters/bugs out?
Solutions - make a screen with no-see-um netting covered with 1/8 inch hardware cloth covered with 1/4 inch hardware cloth that fits over the pipe shown in the picture. There are ways to install threaded rod into concrete, and I would make a frame for the screen that fits down to the concrete and bolts down in at least 3 places around it, ideally use some old inner-tube rubber as a gasket, and I would also advise you use stainless rod, washers and bolts. No matter what sort of building or cover beyond this solution, bugs,
mice, slugs, snakes can get through just about anything if they think there's something they want
2. Problem: Keeping rain and surface water out of the spring.
Solutions - First look as surface water. We've had heavier and more erratic rain in *many* locations, so if you've got the option to do it right, consider the worst possible flood possibilities and consider how you can slow down, divert, and absorb surface water far enough from your spring that the water will be filtered and decontaminated of the worst stuff before it gets to your spring. Animal
poop can make you sick, microbes think animal poop is yummy, so lots of different plants to encourage lots of helpful microbes in your soil, would be my approach, along with managing the slope of the
land away from the spring.
Second, your spring needs a "rain-hat". Plastic bags turn to plastic dust with UV, so, I'm sure you can choose a better option. However, you're going to potentially have to work on this spring at some point, so I would want a hat that's either big enough to work under or is easy to remove. The former owners of our farm built a 4 ft cube with a flat roof which could not survive our wet winters and the whole thing rotted, so I suggest you do better than that, also. You could think along the lines of a small portable
chicken coop that one or two people could lift off - that sounds a lot like what Anne Miller has suggested. I will *strongly* support a sloped/peaked roof, but I've been burned too many times by flat roofs to ever want to go there again (in other words, totally biased against flat in most climates). Similarly, I'd plan for decent overhangs to protect from driving rain, unless you're concerned about really high, gusty winds that tend to rip roofs off if they can.
Third, you haven't mentioned temperature. Are you prepared to build small, let the structure get covered by snow in the winter, and you're sure nothing important will freeze and break at an inopportune time?
Thanks so much for posting the pictures, but of course, you've now given us more questions to ask!
Like what's the dimension of the wooden box in the picture. From the snake, I'd guess 2 ft square?
And what's your budget?
And how motivated are your to approach the issue from an upcycling/scrounging direction?
Or how much do you want this to be *really* inconspicuous in your environment? (Build small and plant stuff!)
If you want more ideas than you know what to do with, you've come to the right spot!