The pale blue River of Parasites emitted twinkling bioluminescence, a phenomenon of bioluminescence in activated biomass.
Shasha and Andor did not travel together, not because they feared the Brain-Eating Parasites; a prepared Magical Beast of the First Power Level could easily expel them from its body. Only Magical Beasts on the verge of death, unconscious, or those with severe bleeding wounds could possibly be parasitized.
Ian dispatched Shasha and Andor on a safer, longer route, also as a contingency plan for later actions—there was more than one river leading to the cold-water interchange area. Should their upcoming actions fail and they need to flee, an underground river crossing from above the interchange area was safer than the River of Parasites.
As for the Pirate Captain, Ian wasn't worried he would escape. Not to mention his missing leg, Ian was certain the man didn't know his way around and needed to wait for them to exit the ruins together.