This paper reports a study of the effects of a collaborative inquiry approach to science on language minority students' (middle and high school) learning. This approach emphasizes involiving the students, most of whom have never studied science before and some of whom have had very little schooling of any kind, in "doing science" in ways that practicing scientist do. This study addresses the question: To what extent do students appropriate scientific ways of knowing and reasoning as a result of their participation in collaborative scientific inquiry? We focus our analysis on changes in students, conceptual knowledge and use of hypotheses, experiments, and explanations to organize their reasoning in the context of two think-aloud problems. The findings indicate that at the beginning of the school year the students' reasoning was non-analytic and bound to personal experience. By contrast, at the end of the school year they reasoned in terms of larger explanatory system, used hypothese to organize and give direction to their reasoing, and ddemonstrated and awareness of the function of experimentation in producing evidence to evaluate hypotheses.