In order to create conditions for students' meaningful and rigorous intellectual engagement in science classrooms, it is critically important to help science teachers learn which strategies and approaches can be used best to develop students' scientific literacy. Better understanding how science teachers' instructional practices relate to student achievement can provide teachers with beneficial information about how to best engage their students in meaningful science learning. To address this need, this study examined the instructional practices that 99 secondary biology teachers used in their classrooms and employed regression to determine which instructional practices are predictive of students' science achievement. Results revealed that the secondary science teachers who had well-managed classroom environments and who provided opportunities for their students to engage in student-directed investigation-related experiences were more likely to have increased student outcomes, as determined by teachers' value-added measures. These findings suggest that attending to both generic and subject-specific aspects of science teachers' instructional practice is important for understanding the underlying mechanisms that result in more effective science instruction in secondary classrooms. Implications about the use of these observational measures within teacher evaluation systems are discussed.