Answer: It's hard to say exactly what it is. There are a number of possible factors. First of all, when you water the plants, try to avoid getting water on the geranium leaves, since this can encourage disease. (Of course if the plant is outdoors, the rain will wet the leaves, but at least you won't contribute to the problem.) Be careful of overfertilizing, especially with a nitrogen-rich fertilizer, since this can lead to succulent growth that is more inviting to pests. (It can also reduce flowering.) Is the container very crowded? This limits air circulation, also encouraging disease, so you may want to space plants further apart. Apply a layer of mulch to the soil surface, to minimize soil borne disease spores from splashing onto plant leaves. Finally, if only a few leaves are affected, you might want to remove them as a precaution.
I hope this helps.
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