If you’re looking for the short TL;DR (too long didn't read) answer to this question, it’s yes, you can.
In fact, yes, you probably should. It’s recommended that you use the pump between 5-12 hours a day, depending on the weather.
If you keep the solar cover on, all you do is keep the heat in the water while the pump does its thing.
Now, it’s true that we can see why people would ask this question.
The combination of something that pumps and filters the water and something that keeps it warm could, in the right circumstances, act as a potential science experiment, boosting the growth of bacteria and algae.
But the point is that using a technology that heats the water without some technology that keeps it moving is actually far more likely to create the kind of chemical soup you’re thinking of, because static warm water allows bacteria and algae to really get down to the business of feeding and reproducing.
If you keep the eater moving, it’s less likely they will have the resources they need to build and grow at anything like the same speed.
Your pool’s pump runs the filtration system that stops your pool from turning with indecent haste into a stagnant pond.
What Does A Solar Cover Do?
A solar cover is basically nothing more than a large thermal blanket that you put over your pool, specifically for the purpose of keeping in the heat that your heater has produced, and that has been circulated throughout the water in the pool by the pump.
It also acts to transfer heat from the sun to the water, so your heater doesn’t have to work so hard and cost you so much money.
And if you need a third reason to keep your thermal cover on when you’re not actually in the pool, it acts as a barrier between any dirt and debris that wants to land in your pool, so your pool water stays cleaner, longer.
It also reduces evaporation from your pool (up to 2 inches a week!), stops the pool chemicals from heading into the air along with the evaporated water, and, by warming the water, can extend your pool season by a couple of weeks longer than other people’s.
In fact, by keeping your solar cover on the pool when you’re not using it, you can probably extend your pool season through to the end of fall.
Late fall pool fun while everyone else is shivering and covering up their pool for the winter? That’s priceless.
None of this is affected in the slightest by the pool pump being on for its regulation 5-12 hours each day. Again, the actions of the two systems are entirely separate – one keeps the water warm, the other keeps it moving.
All you have then is warm, moving, probably significantly clearer water than you otherwise would have. Where’s the bad?
How Does A Pool Pump Work?
OK, we’ve said that a solar cover is essentially little more than a blanket to keep the water warm and cut down the energy you need to pay for in order to keep It at a luxuriant temperature.
What about the pool pump? How does that work?
Usually, pool pumps are centrifugal pumps. That means they use the power of centrifugal force to make water move through a system.
They pull water into an inlet, and they push it out through an outlet. Once the water has been pulled into the inlet, it’s in the filtration system.
Think of a coffee maker, or a leaf tea strainer for that matter. Then imagine a whole set of strainers, one after the other, the holes in their wiring getting smaller and smaller, until finally there’s a muslin cloth.
Water will of course always go through any hole, so the water passes through all the filters in the system.
But things that are bigger than water – stones, grit, debris, etc – get trapped, and can’t move beyond a certain point in the filter.
The result? Much cleaner, filtered water by the time it gets to the outlet and is recirculated into the pool.
Obviously, the more you use the pool – the longer the water is exposed to the air, and to airborne contaminants and grit, the more you need to use the pool if you’re to keep the water as clean as you’d like to imagine it is when you’re swimming in it.
And likewise obviously, the more often you’re going to need to clean out your filters of all the grit and contaminants.
But it’s advisable to run the pump for between 5-12 hours a day, whether or not anyone’s using the pool during pool season.
You may not be in the pool, but you can never tell what else might be, after all.
Why Pump When You’re covered?
Now, that does suggest a reason why people would argue you shouldn’t run the pump while the solar cover is on.
If the solar cover is keeping out contaminants, then there should be nothing to get trapped by the filters, and so you shouldn’t need to run the pump. Right?
We can see why you’d think that, but no.
Firstly, the solar cover is not tied tautly over the surface of the pool, it simply floats there.
That means it’s by no means an airtight or perfect seal, and that in turn means it can let in at least some contaminant – which, if your pump is running, will be dealt with when it meets the filters in the system.
And secondly, there’s that whole stillness=potential bacterial barbecue thing. If there’s bacteria or algae in the water, then simply turning up the temperature will give them the conditions they need to feed and breed.
And yes, sadly, there will be bacteria and algae in the water, because those little Darwinian geniuses are often too small to be stopped by the filter system.
Which, yes, is exactly why you need to shock your pool on a regular basis).
So if you’re going to keep your solar cover on the pool, it’s actually more necessary than usual to keep your pump running, because very little of the heat in the water is able to escape through evaporation.
As we said at the start, it’s perfectly safe to run your pump while you have your solar cover on. In fact, as it turns out, it’s actually a really useful thing to do.