The first place to look, in your job as plant detective, is the potting mix. Is it very coarse textured and fast-draining? Most commercial potting mediums are almost entirely peat, which can make them sludgy over a bit of time. Those potting mixes can cause over watering issues, as well as develop dry pockets from improper watering (little sips at a time).

Jean001, Thanks for the response I live in the SF Bay area - Fremont, CA. The soil type is clay here. Fertilizer. I have been using only Organic Citrus fertilizer for this tree. I used E.B. Stones Oragnic citrus fertilizer - 7-3-3 last year. This year I have been using Jobe's Organic Citrus fertilizer - 3-5-5. I typically fertilize once a month during spring and summer. I don't fertilize from Oct-Mar. Not sure if that is ok. I follow the directions on the package and I have been adding 1.5 cups each month for this tree. Two weeks back I added 1/2 cup of Iron supplement - Dr.Iron. I don't think it is Chelated Iron. Other than this I have not added any other supplements.The leaves are deformed and I thought I might have a spider mite infestation. So I'm spraying Insecticide soap to this tree once a week for three weeks now. Irrigation If we do not have rains which we have been having a lot lately, I typically water once a week for 5 minutes spring and summer. Also I stop after 5 minutes because the water starts to stagnates around the tree after 5 minutes. But it drains after a minute or two.Not sure if this means the drainage is bad. I'm not sure about the moisture content, How do I check it?

OK, from what I read, it mostly peat and has a little perlite..But no bark... If it were me, I would make sure to re pot into a pot just one size up from the root ball so it dries out faster and make sure to flush at least twice a month with fresh water...If you find that the mix is still holding moisture more than 5 days, then I would re pot it into a clay pot....This will force you to water more frequently since it will dry out faster, help prevent rot, and allow you to flush your mix from all the salt deposits more often..It will also force you to re pot every few months before the mix compacts again....Re potting again will not hurt, just make sure you remove as much as the old mix as possible carefully... If you can find bark as Laura suggested, even better! I would leave the dirt out of your mix and just use the bagged...............Glad you came here for help..Hopefully you will stick around and let us know how it goes. Can you take a pic of the ingredients in the fertilizer? I looked that up and it does not say at all..

A two year old lemon tree should be about 2 to 3 feet high. Are you fertilizing the trees? They are "growing" in much too large of a container, and as Johnmerr pointed out you have them in a poor light situation. Citrus require fertilizers with higher levels of both nitrogen and potassium. You can use organic fertilizers if you wish, but citrus perform much better with conventional fertilizers. Wishing a good future to these trees.