Environmental factors are thought to strongly influence the distribution and predictability of the coastal distribution of southern right whales (Eubalaena australis) off South Africa. Preferred habitat had generally shallow sloping sedimentary floors and was characteristically protected from open ocean swell and prevalent seasonal winds. This study investigated whether habitat choices at smaller scales (within bays) were similar. Fine scale distribution patterns (GPS) from three years' surveys (1997, 1999, 2000) were analyzed separately within the three main concentration areas St Sebastian Bay, De Hoop, and Walker Bay (containing ∼73% of cow-calf pairs and ∼49% of unaccompanied adults in the whole survey region). Whale density at this scale of within particular bays did not correlate well with predicted variables, but Chi-squared analysis strongly supported results at broader scales, in all bays. Post-hoc“choice” tests between similar areas differing in only one variable revealed that cow-calves preferred (presumed) sandy substrates and especially protection from swell. The strength and predictability of preferences shown at fine scale (where individual movement and weather variability could have great influence) provide strong support for findings at larger scales and emphasize the importance of environmental factors in the habitat choice of wintering right whales.