This quasi-experimental study evaluated middle- and high-school science teachers' implementation of three-dimensional (3D) instruction as defined by the "Next Generation Science Standards." Teachers participated in a long-term professional development (PD) program designed to increase their use of inquiry-based science instruction. We describe our semi-quantitative adaptation of the Educators Evaluating the Quality of Instructional Products: Science rubric version 2 (SQ-EQuIP) to facilitate the longitudinal evaluation of teacher practices with 3D instruction. SQ-EQuIP evaluations revealed that after two years, 80% of PD teachers implemented lessons where students were explicitly and coherently engaged in 3D learning, compared with 22% of comparison teachers. Further, in several cases lesson materials that should support student engagement in 3D learning were not implemented with fidelity. This discrepancy implies that PD developers must use the EQuIP not only to assess lesson or unit plans as intended by its creators, but to also evaluate the implementation of these materials from students' perspective. The small sample size restricts claims of significance. However, observed trends between teacher groups indicate long-established best practices designed to increase teacher use of inquiry-based practices may also positively impact teacher use of 3D instructional practices.