Soak in 2% bleach or Milton for at least 15 minutes.
Use a thin bottle brush to scrub out - not forgetting the spout. (An old toothbursh is good for the latter)
Rinse thoroughly at least 5x.
You can cut down algal growth by keeping the bottles wrapped in paper/cardboard...however this will not stop bacterial growth so better to just disinfect the water bottles on a weekly/fortnightly basis.