Hi Chris,
Hope you are doing well.
I used to use AEM3D a lot not long ago and I found a small error within the model. I thought maybe sharing it here might be helpful. The model adds a large value of concentration (e.g. phosphorus) at the cells with inflow that dry out. When there is an inflow cell and the water surface falls below it, the model assigns a large value of concentration that exists in the domain into the model.
Thanks,
Alireza