This study deals with the implementation of a web-based collaborative inquiry (WISE) project in secondary science education and unravels the contribution and challenges of this learning approach to foster students' motivation to learn science, and its relation with student and class-level characteristics. An empirical mixed methods study in 13 secondary science classes was conducted, involving 220 students. Students' motivation was quantitatively studied based on the self-determination theory, and it was hypothesized that web-based collaborative inquiry can be considered as a need-supportive environment, which in turn can foster autonomous motivation and decrease controlled motivation. In addition, qualitative analyses were conducted on students' experiences and future preferences regarding the WISE project. It was found that the hypothesis of an increased autonomous motivation only holds for general track students. Moreover these students were significantly more positive about web-based inquiry in science education compared to students from a science track. To conclude, we describe how the learning environment can be improved to satisfy students' basic needs and improve good quality motivation for science learning.