Science education aims at developing students’ knowledge of scientific concepts and principles. However, students differ in their prior knowledge and cognitive skills and thus follow different learning pathways. We examined whether and how experimentation skills predict elementary students’ pathways of conceptual knowledge development in science education. First to sixth grade students (N = 1275) received 15 lessons of inquiry-based classroom instruction on the topic “floating and sinking”. Students’ experimentation skills were assessed before instruction. Their conceptual knowledge about floating and sinking was assessed before and after instruction. Latent profile transition analysis, a markov chain mixture model for continuous longitudinal data, revealed that students with higher experimentation skills were more likely to develop proficient and consistent knowledge of floating and sinking. We discuss theoretical implications of this finding, advantages of mixture models to examine conceptual knowledge development, and implications for science education in elementary school.