I know that it has been a long time since OP posted about this topic, but I will reply for posterity.
I have a kidney transplant. At first I was very concerned about the immunological response to diving in different waters. I think those still remain, especially in and around freshwater lakes with agricultural activity.
Every situation is different, but I have participated in blackwater lake dives without problem.
That being said, to mitigate infection, I use a full face mask to avoid ingesting water. I also use doc's pro plugs in my ears to prevent top water suspended particles from entering my ears. Additionally, I avoid peeing and farting in my wetsuit. I know that is crude, but you want to avoid your muous membranes from coming into contact with bacteria and protozoans as much as reasonable.
As far as using prophylaxis, they should not be used according to my doctor. Flagella is the name of an anti-protozoan that is commonly used in post-op transplant care protocols. It may help, but my doctor advises against using it in my situation.
It should be understood that I am extremely cautious about these things to the point of irrationality. In reality, people swim in dirty lakes with transplants all the time. I just like to take "an ounce of prevention" approach.