small rust colored spots? that might be the fungal disease simply called rust. Treatment is harsh- trim off affected leaves, dunk plant in a 10% bleach solution, let dry a couple of days, and replant. Or that is what worked for me, when my pelargoniums got this. (I am assuming it is a pelargonium, which is commonly called a "geranium". True geraniums are perennials, and would be planted in the ground. Check the FAQs if you aren't sure ;-)

Larger brown spots on occasional leaves is another disease, (name escapes me right now,) but those leaves can simply be pulled off, and discarded. Usually that won't affect the whole plant.
Jean

That sounds very drastic and my plants are 2-3 foot high. Not only are they rusty but they are also leggy and do not look healthy to me either. YES they are green and strong they get plenty of water as they sit ontop of a water run off after a black water recycling process. Question could they be getting too much fertiliser and too much water, BTW they are planted in a clay soil. Should I try some clay breaker on this also ??????