Promoting the development of students' scientific inquiry capabilities is a major learning objective in science education. As a result, teachers require effective assessment approaches to evaluate students' scientific inquiry-related performance. Teachers must also be able to offer appropriate supplementary instructions, as needed, to students. Scientific inquiry capabilities should be assessed by evaluating students' scientific inquiry portfolios in actual hands-on experiments. Although virtual laboratory systems can reduce the cost of conducting scientific inquiry experiments, the manual portfolio assessment approach is still difficult and time-consuming for teachers. Therefore, in this paper, in order to provide students with personalized learning guidance concerning not only the conceptual knowledge, but also the high-order, integrative abilities of scientific inquiry, an Online Portfolio Assessment and Diagnosis Scheme, called OPASS, was proposed to assist teachers in automatically assessing and diagnosing students' abilities as they relate to scientific inquiry performance. Personalized diagnostic reports were generated by employing the rule-based inference approach, which diagnosed learning problems and provided corresponding reasons and remedial suggestions based on teacher-defined assessment knowledge of the scientific inquiry experiment. For the evaluation, experimental results showed that the OPASS was helpful and beneficial for both students and teachers. (Contains 13 tables and 11 figures.)