Watering twice a day is way too much.

You should only bottom water when the top 2/3 or 3/4 is dry. This looks to be your probem with your yellowing leaves in your first picture. From what I can see, seedlings that big in that contanier would need watering 1 or 2 times a week... no misting.

Not too sure about the brown spots.

Sleepy, Dave, oilpainter.. are you out there? What do you think?

What do you mean bottom fertilizer with a spray bottle? You may have burned the leaves if you sprayed them with the fertilizer, hence the brown spots...

Keriann~

Thank you for your reply!

I'm just a little shocked .. Should I really let the soild dry out to that depth?? The cells are rather small (maybe 2.25 inches tall, 1.5 inches wide). I'm afraid if I let the top 2/3 to 3/4 dry out, then very little room will be left for the roots, which need more moist soil ... Or am I mistaken?

Also, I mentioned that I bottom-water by using a spray bottle and shooting a gentle stream into the holes at the bottom of each cell until they reject the water (about 3-5 squirts later).
So when I fertilized them, I mixed the solution and put it in the spray bottle, and then spritzed them through the bottom holes as I normally do. The last time I did this was Tuesday or Wednesday.

I agree with Keriann. Yes, you should really let them dry out. Matter of fact, once my seedlings are as big as yours, I let them dry out pretty much all the way before I water again. You can tell they need watered when you pick up the flat and it feels light as a feather. Then after you water, it's much heavier.

Your method of bottom watering is quite unique, I must say. I think that most folks bottom water the way I do, which is to say setting the cells or cups into a tray of water and letting the plant absorb as much as it wants until you see moisture on the surface of the soil (usually takes anywhere from 5-20 min). Now, I can't say for sure what positive or negative effects your method of watering might have, except that it sure sounds like a pain in the hiney to me, and I somehow doubt that the soil is getting properly saturated. You want to simulate mother nature; a soaking rain. Then you want to let the soil dry out. That's how it is in nature. Roots need water yes, because the plant needs water, but then they need to dry out and get oxygen. Damp soil all the time = no oxygen to the roots. Now, I can't say for certain what part of your program is causing your issues, but I would start bottom watering them as described by letting them absorb water sitting in a tray. I think you will find that using this method, you should only have to water every 3-4 days, or less. I would lay off the ferts for a while, and then make sure only to fertilize when the soil is already damp, or you will burn the roots. I just mix the fert with water, then pour into a tray and bottom water as usual. Give this a shot, see if that doesn't help.

The problem with watering your way is like the others say the soil is not being evenly watered and what is is saturated with no oxygen to the roots. You are a prime subject for root rot, which is just as bad as damp off.

Yellowing of leaves usually means one of two things--too much water or lack of fertilizer.

The proper way to water is as others say--to let the soil dry out and then bottom water and then don't water again until the soil dries. A plant will recover from lack of water and do it rather quickly. Too much water is sure death and that is a common mistake that new gardeners make. They think that a plant has to be wet all the time--it doesn't.

When you fertilize water first and then fertilize so you don't burn the roots.

Right now you need a fan on your plants to dry them out

Thanks ladies, you explained better than I did!

Keep us updated Laura :)

Keriann~

Thank you also for your replies, sleepy33 and oilpainter!

To sleepy33 --
Interestingly enough, I started my "unique" method of watering after being dissatisfied by regular bottom-watering, as you described. My problem is that my seedlings are growing in my crawl space (which is finished, if you can believe that)! But it's still probably a breeding ground for mold. So when I bottom-watered the cells until the top of the soil started becoming moist, they wouldn't dry out fast enough in time to prevent mold growth. Mold sprouts in that darn crawl space in a matter of, like, 12 hours. It's ridiculous! Even a fan doesn't seem to help.

So I started using the spray bottle, because I knew it would saturate the bottom layer of soil quickly (and hopefully seep upward gently after the watering) and never reach the topmost layer of soil. So far it's worked pretty well -- I haven't seen too much mold in a while. But I realize I'm also no expert!

Do you think that if I maintain my current watering system, but simply start watering less (until a substantial chunk of soil is dry), that I might be successful in preventing root rot or any other maladies? I'm just so afraid to go back to the "normal" method of bottom-watering, because it only led to mounds of mold in my seedling trays. :(

And oilpainter --
Yes, I made sure to water first before fertilizing. Luckily I knew that much! lol.

Thanks again to all three of you for your advice. If you have any other thoughts, please share! And I'll definitely keep you updated. :)

Boy, I just don't know; the only thing you could do I guess is give it a try. I don't know where in zone 5 you are, but maybe you could start transitioning these guys outside. That would allow you to water 'normally' and avoid mold.