This study investigated the understanding of diffusion, osmosis and particle theory of matter concepts among 192 pre-service science teachers in Saudi Arabia using a 17-item two-tier multiple-choice diagnostic test. The data analysis showed that the pre-service teachers' understanding of osmosis and diffusion concepts was mildly correlated with their understanding of particle theory. We also identified 18 common alternative conceptions in these topics. The findings suggest that greater time and attention needs to be invested in the teaching of particle theory for Saudi pre-service teachers to ensure their scientific understanding of diffusion and osmosis concepts, so that they can help students understand the concepts better.