The U.S. Gulf Coast’s most important industrial waterway partially reopened on Monday after it was polluted with cancer-causing benzene and toxic runoff from the region’s worst chemical disaster in more than a decade.

A two-mile (3.2-kilometer) stretch of the Houston Ship Channel’sthat’s been closed for three days will be open during daytime hours while the clean-up continues. Pilots have been ordered by the U.S. Coast Guard to stay at least 40 minutes apart so each vessel can be inspected to ensure it’s not dragging oily residue through the water.

The partial reopening means that oil refiners, chemical makers, grain...