Hi, great question. I have 25 chickens who love to scratch and dig to China. Every time I go out to check the girls, their water is dirty. I also have water buckets at different levels and they too, get dirty. I just clean each one several times a day and make sure to clean up any poop droppings, to keep things cleaner and the fly population down. Sometime chicken poo can be watery or mustard colored. This is OK. But if it happens all the time, you might want to have a vet check things out.
Oh and you should keep the nesting boxes very clean. Eggs with chicken poo can carry disease. My girls will wait until I go and clean out any mess in their nesting boxes before they will lay any eggs. When they see me coming they know they will get treats to eat while I clean their pens. The girls will line up and as each box is cleaned and fluffed up, they will begin laying. And if I am too slow, they let me know about it.
I think if you keep the area clean and free of poo and get rid of any cracked eggs and give them fresh water and food every day, then the eggs are safe to eat.
Good luck