This study was undertaken to investigate the progress in operational scientific literacy skills through demonstrating cognition associated with undertaking scientific processes. Scientific literacy is taken here to mean utilising science knowledge and skills, particularly with relevance to creative problem solving and making reasoned decisions in real life situations. The instrument was compiled based on a review of relevant international literature, plus competences emphasised in the Estonian science curriculum. Items in the instrument followed the levels of the Structure of Observed Learning Outcomes (SOLO taxonomy) and all tasks in the instrument were contextualized to relate to real life. A stratified sample of students from 44 schools gave a data set with returns from 1128 beginning of 10th grade students and 946 end of 11th grade students. Findings suggested that there was no sufficient shift from one grade to another in operational skills such as giving scientific explanations, problem solving and justified decision making. Although students did gain more knowledge and the expectation was that students would enhance their operational skills for scientific literacy, this was not reflected in their competence to solve problems. This suggested there was a need to re-think science teaching and learning approaches as well as the manner in which science was introduced to students.