Given the need for effective problem-solving and decision-making skills in students entering the science, technology, engineering, and mathematics (STEM), and food, agriculture, natural resources, and human sciences (FANH) workforces, it is critical to create undergraduate learning environments that foster these skills through best practices (active learning). Here, we use the Classroom Observation Protocol for Undergraduate STEM (COPUS) to characterize instructional practices in Food, Energy, and Water Systems (FEWS) undergraduate courses at one institution, including the use of active learning strategies. Specifically, we investigated the types of instructional strategies used and how they impact the development of students’ systems thinking and decision-making abilities. We found that, similar to other STEM and FANH studies, traditional lecture strategies were most common overall (62.5%), but longer class periods consisted of more active learning strategies (89%) than shorter class periods (28%). However, we found that student outcomes generally decreased in longer class periods. We believe longer class periods allow instructors time to incorporate active learning strategies. However, overall course and curriculum structure and organization may have a more holistic impact on students as compared to individual factors. Further empirical study should account for the quality and occurrence of best practices in undergraduate classrooms.