Empty the water out of the pan. Pots shouldn’t be standing in water. By all means water from the bottom if you wish but don’t put in more water than the pots can take up in a short time.

If there is standing water that the plants are sitting in, I have to assume that at least the soil in the bottom of the pots is waterlogged. So while algae won't hurt anyone, plants become stressed in waterlogged soil. Lack of soil oxygen leads to reduced nutrient uptake. Of course, the algae is growing using the nutrients that the plants should be getting.

I have used patio pickers with a lot of success. They have a water reservoir built in. So do a lot of seed starting kits - it is really nice to not have to water as often and be able to leave town for a week with out finding someone to water (which I am doing twice before plants go outside into the garden.

Basically I am going to keep them in water - I let it dry out BUT the 3'x3' pan is pitched to center so even water from the top leaves some water in the middle that is nearly impossible to get rid of.

As long as it is ok for plants then I am not worried about it. I have watered from stuff that had algae often with no bad results - but never had algae always in the water......

So are you telling us that these are a special self-watering type of container? The way you worded the question that wasn’t clear. It sounded as if you just had ordinary pots sitting in a dish of water.