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The study investigates the effect of an interactive simulation with embedded inquiry support, which was seamlessly embedded within the simulation, on students' scientific literacy and school science achievement, and explores the relationships among prior school science achievement, inquiry processes and scientific literacy. A total of 49 eighth-grade students at a public junior high school in northern Taiwan participated. Data collected include the students' pre- and post-scores for school science achievement, logging data that indicate their inquiry processes, and pretest, posttest, and delayed-test data that measure their scientific literacy. The results provide evidence that the designed simulation and inquiry support had a long-term effect on the students' scientific literacy. Replacing conventional teaching with inquiry activities did not harm the students' school science achievement performances. Moreover, compared to school science achievement, students' scientific literacy seems a better predictor of their inquiry behavior, especially in the aspect of making conclusions. Analyses of the students' inquiry processes indicate that the so-called low science achieving students conducted more data analyses than the other students, and demonstrated adequate inquiry engagement. The students with middle level school science achievement demonstrated the most active engagement in inquiry and showed good gains of scientific literacy after the learning. These results indicate that a guided inquiry learning environment can support students with different levels of school science achievement to highly engage in science inquiry. Implications and future studies are discussed. • The designed simulation and embedded inquiry support had a long-term effect on the students' scientific literacy. • Compared to school science achievement, students' scientific literacy seems a better predictor of their inquiry behavior. • The low science achieving students conducted more data analyses and demonstrated adequate inquiry engagement. • The middle-level achieving students demonstrated the most active engagement in inquiry and gains of scientific literacy. [ABSTRACT FROM AUTHOR]