C. whitakeri seems to be dependent on dry and stony habitats, with sparse vegetation (i.e., steppe or subdeserts). It is also found in sandy coastal dunes. The species shelters among rocks and in rodent burrows.

Crocidura whitakeri is endemic to Atlantic and Mediterranean parts of North Africa; Western Sahara (R. Hutterer pers. comm. 2007), Morocco, Algeria and Tunisia (see references in Wilson and Reeder 2005). It also occurs on Ceuta and Melilla (Spanish Northern African Territories) (L.J.P. Muñoz pers. comm. 2007). It has been recorded from sea level to 1,800 m and is especially well distributed along the Atlantic front of Morocco. It seems to be absent from most of Algeria's coastal zone, where its distribution runs along southern border of the Saharan Atlas mountains. There is one record from coastal Egypt (Wilson and Reeder 2005).

New localities have recently been found in southern Tunisia. Some data are also available from western Libya, where it was reported as Crocidura russula but may be C. whitakeri(R. Hutterer pers. comm. 2007).