Thanks for the question.

I believe that it is unlikely that these holding tanks would lead to the spread of fungal diseases. The fungal spores would not be expected to survive under those conditions. Bacterial blight might be a different story. I would suggest that you contact the Minnesota Pollutions Control Agency to determine what type of tests might be performed on your water. See:

https://www.pca.state.mn.us/air-water-land-climate/water-quality

As you indicated, controlling algal growth in irrigation holding tanks is important to maintain water quality and system efficiency. Here are some of my thoughts:

1). Algae thrive in sunlight, so reducing light can limit their growth. Try covering the tanks with opaque tarps, lids, or floating covers. Can you place the tanks in a shaded area?

2). Have you considered the installation of some type of filtration system? For example, mechanical filters can help remove suspended particles, including algae, from the water before it enters the irrigation system.

3). Installation of an aeration system for the water would reduce the conditions that promote algae growth.

4). As a last resort there are algaecides that are designed to kill algae. Choices include copper-based algaecides, hydrogen peroxide algaecides, sodium carbonate peroxyhydrate, or bleach. Unfortunately some or all of these may not be safe to use on gardens whose products are intended for human consumption.

See the following:

https://blog.enduramaxx.co.uk/5-tips-to-prevent-algae-growth-in-drinking-water-tanks

https://www.extension.purdue.edu/extmedia/ho/ho-247-w.pdf

https://itppackaging.com/how-to-prevent-algae-growth-stored-in-water-tanks

Good luck. Please get back to us with any further, related questions.