Anopheles balabacensis inhabits forested areas. The immature stages are principally found in shaded temporary pools of stagnant fresh water, including puddles, animal footprints, wheel tracks, ditches and rock pools. Larvae have been collected in animal wallows in primary forest in Sabah. They are sometimes found at the edges of swamps, streams and rice fields, and less frequently in containers (e.g. coconut shells, cocoa pods, barrels, drums and buckets) in shaded, partially shaded or sunny locations.