Several studies have highlighted that reading comprehension is determined by different linguistic skills: semantics, syntax, and morphology, in addition to one’s own competence in reading fluency (accuracy, speed, and prosody). On the other hand, according to the Linguistic Interdependence Hypothesis, linguistic skills developed in one’s own native language (L1) facilitate the development of these skills in a second one (L2). In this study, we wanted to explore the linguistic abilities that determine reading comprehension in Spanish (L1) and in English (L2) in Secondary Education students. To do this, 73 Secondary Education Students (1st and 3rd year) participated in this study. The students carried out a battery of tasks in English and Spanish, all of them related to reading comprehension (expository text) and different linguistic skills, which included syntactic awareness tasks, synonymy judgment tasks (vocabulary), and morphological awareness tasks. The results indicated a positive correlation between linguistic competencies in both languages (indicating a transfer effect between languages), which were determined by school year, with a lower performance in the 1st year than in the 3rd year. Moreover, we found more skills with correlations in English reading comprehension than in Spanish. Finally, reading comprehension in L1 was mainly explained English reading comprehension, while English reading comprehension was predicted by grade, and syntactic awareness, as well as Spanish reading comprehension. This could be explained by the different levels of exposure to L1 and L2 of sample subjects, as the linguistic variables have different influences on the reading comprehension of both languages.