First guess would be mold/fungus which spreads due to poor watering practices.

Simple rule of thumb;

Most molds/funguses are in the soil.
When watering never let the water splash on the plant.

Don't spray water on your tomato plants unless you absolutely have to.

If you don't have drip irrigation I highly recommend you install one. It's cheap and lasts for many years.

I'm sure many will disagree with my on what I'm about to write but here goes.

Spray the plants with Daconil to protect them from soil born molds and funguses.

If you have a serious insect problem use a real insecticide that is rated as safe to spray up to the day of harvest. I would recommend "Spectracide Triazicide Once and Done".

Thisisme,

Thanks for your insight; I was thinking I have had had fungus gnats, but wasn't sure about the mold/fungus part. The affected plants have been removed and I will be making some adjustments to my watering. I do have a drip line, but I temporarily took it out when I built the raised beds.

Thanks :)

Silverchez many vegetables like peppers, squash and tomatoes are susceptible to soil born molds and funguses. Once infected there are all kinds of Plant Diseases named for them. ItâÂÂs the simple things that allow them to get infected. ItâÂÂs much easier to prevent than it is to get rid of which is why when it comes to tomatoes good plant culture should always be stressed.

Fungus gnats are more often than not due to over watering. So you may want to back off on the watering just a little. Or, perhaps the drip irrigation will solve that problem too.