Introduce what project-based learning is to your students. This may be a very different style of teaching science than your class has ever experienced. On the first day of class, explain to the students that they are expected to be active participants. In your class, they are not just students. They are scientists and will be expected to act accordingly.
Emphasize that the experiment must come first. This is one of the tougher aspects of project based teaching. In "normal" science classes, students learn a prescribed lesson and then do an experiment that teaches them about that lesson. Start with a series of projects on the lesson and have the students write down what they are learning. This will help them remember the lesson much better than if they are told the result and then given an experiment that produces an outcome they already know.
Allow the students access to the grading rubric before they begin their experiment. This should apply for all experiments, but especially for the final project. Just like in other science classes, the students will be expected to perform similarly to their peers and in accordance with state expectations. The assessment will not differ in form than other science classes. Yet the assessment is much more important in a project-based learning environment because a large percentage of the student's grade depends on the project he completes.
Assign a project for students to turn in at the end of the year. This can often take place in a science fair. The subject matter must be broader than an individual lesson and incorporate an array of scientific knowledge from throughout the class. Give students the choice of the topic, and let them know they can center the projects around their own interests and abilities, and involve other subject matters, such as art or music, if they desire. Make sure the students "show all work", meaning they accurately portray resources and references.