18 month old son drank some horse manure water?

So my son was w/ my husband and I up at the barn. I noticed him playing in a puddle, so I swept it out the door. When I got back from putting the broom up (only a few steps away), when I turned around he was on his hands w/ his mouth in the little puddle left. I am so scared of what can happen to him. Dr.'s nurse just said he will more that likely get the runs and maybe parasites. She didn't tell me how long it takes for parasites to get started and when we can test him. Gads it really does only take a second w/ boys. Can he get Geriardia or Salmonella?