Intuitive knowledge seems to influence human decision-making outside of consciousness and differs from deliberate cognitive and metacognitive processes. Intuitive knowledge can play an essential role in problem solving and may offer the initiation of subsequent learning processes. Scientific discovery learning with computer simulations leads to the acquisition of intuitive knowledge. To improve knowledge acquisition, particular instructional support is needed as pure discovery learning often does not lead to successful learning outcomes. Hence, the goal of this study was to determine whether two different instructional interventions for scientific discovery effectively produced intuitive knowledge acquisition when learning with computer simulations. Instructional interventions for learning with computer simulations on the topic 'ecosystem water' were developed and tested in the two well-known categories data interpretation and self-regulation using a sample of 117 eighth graders during science class. The results demonstrated the efficacy of these instructional interventions on learners' intuitive knowledge acquisition. A predetermined combination of instructional support for data interpretation and for self-regulation proved to be successful for learners' intuitive knowledge acquisition after a learning session involving the computer simulation. Furthermore, the instructional intervention describing and interpreting own simulation outcomes for data interpretation seems to be an effective method for acquiring intuitive knowledge.