Students participated in a study (n = 98) investigating the effectiveness of three types of annotations on three learning outcome measures. The annotations were designed to support the cognitive processes in the comprehension of scientific texts, with a function to aid either the process of selecting relevant information, organizing the information in memory, or integrating information with prior knowledge. Learning outcomes were measured by assessing student recall of facts, comprehension of the text, and mental model construction. Results show that different types of annotations facilitate different learning outcomes. In addition, we found that, compared to having only one type of annotation available, multiple types of annotations resulted in a higher cognitive load that resulted in lower performance, especially in tests of higher-level processing. This effect was stronger for low-verbal-ability learners, who showed lower performance in treatments with multiple types of annotations than high-verbal-ability learners.