One of the goals of secondary science education is to help students develop skills related to scientific inquiry. However, the results of previous studies have shown that students have difficulties in identifying problems, formulating hypotheses, drawing conclusions, and designing experiments. The main objective of this contribution is to indicate the situation in the southeast of Spain in this regard, comparing progress throughout secondary education. Four instruments were designed based on specific problematic situations in biology that were solved by 260 students from three different educational levels (12, 14, and 16 years old). The results show that high school students learn very little in terms of the development of the aforementioned skills and have difficulty understanding their meaning in the science texts used in the classroom. In this paper, some of the reasons that could explain this situation are analyzed and suggestions are made as to how the teaching of the desired skills could be improved.