The study explores the impact of certain linguistic factors on phonological awareness ability in the second language. This study examines the effect of three linguistic factors on Saudi university students’ L2 phonological awareness: the linguistic environment (single vs. clustered), the linguistic affiliation of the phoneme (novel vs. non-novel), and the phonological representation of the lexical item that contains the target phoneme (real-word vs. non-word). The linguistic factors that are examined and controlled in this study represented essential differences between the participants’ L1 and L2, hence highlighting the effect of L1-L2 distance. The participants were 48 university students majoring in English language. Two phonological awareness tasks were administered, a phoneme deletion task and a phonological judgement task, to test phonological awareness at the phonemic and phonotactic levels. The results showed that the linguistic environment of the phoneme had a significant impact on the participants’ L2 phonological awareness. The linguistic affiliation of the target phoneme was another linguistic factor that affected the participants’ L2 phonological awareness. Their perception of novel L2 phonemes was considerably poorer than non-novel phonemes. This result confirms the validity of the linguistic affiliation hypothesis in explaining phonemic awareness in L2. Additionally, the results revealed that the quality of the phonological representation plays a significant role in the participants’ performance on the phonological awareness tasks in L2 and that the lexical status of the item affected this underlying phonological representation. The findings of this study offer theoretical and practical implications for the acquisition and teaching of a second language.