Do you have any issues with shellfish at your intakes? Have you found ways to control these populations?
That's not an issue I see as being a problem for my area, but I did recently run into an article about how they were using ultrasonics with ballast tanks for shipping to control shellfish populations. Merging that technology into treatment would certainly be interesting. Here's the paper if you want to take a look. http://www.sea-acustica.es/WEB_ICA_07/fchrs/papers/ult-11-002.pdf
As an added benefit, ultrasonics might be useful for algae control as well.