Q.African Lilies
My African Lilies bloomed beautifully last year and again this year. After blooming this year the foliage began to turn yellow with black spots. They don’t seem to be receiving too much water. Could it be a nutrient deficiency? They have been planted for only two years as the house is new and these lilies were in the ground when we moved in.

This sounds like Antracnose Fungus.
Keeping the plants healthy and correctly watered and fertilized will help.
Remove the diseased or dead plant material.
It is possible the plants need to be divided to open up and provide some air circulation.
Here are some links with more information.
https://www.gardeningknowhow.com/plant-problems/disease/anthracnose-disease.htm
https://www.gardeningknowhow.com/ornamental/bulbs/agapanthus/diseases-agapanthus-plants.htm
https://www.gardeningknowhow.com/ornamental/bulbs/agapanthus/agapanthus-flowering.htm