The study explored science teachers’ perceptions of Scientific Investigations (SI) and their classroom practices in South Africa. An explanatory sequential design using qualitative and quantitative approaches was used. Qualitative data were collected first using interviews and classroom observations, followed by quantitative data using a questionnaire. Qualitative data were thematically analysed, whereas quantitative data were analysed using descriptive statistics: percentages; and inferential statistics: t-test; Analysis of Variance (ANOVA); and Honest Significant Differences (HSD) Tukey. Three themes emerged from qualitative data: different perceptions of SI, challenges in teachers’ skills, and resource challenges in schools. Quantitative results show teachers from differently resourced schools had diverse perceptions of practical work, inquiry, and SI (ANOVA, p=.04). These perceptions included confining hands-on activities to practical work, and limiting inquiry to oral questioning. Teachers’ challenges in facilitating SI included inadequate skills and a lack of resources. These findings have far-reaching implications for learners’ science achievements and policymakers.