Comprehending digital content written in natural language online is vital for many aspects of life, including learning, professional tasks, and decision-making. However, facing comprehension difficulties can have negative consequences for learning outcomes, critical thinking skills, decision-making, error rate, and productivity. This paper introduces an innovative approach to predict comprehension difficulties at the local content level (e.g., paragraphs). Using affordable wearable devices, we acquire physiological responses non-intrusively from the autonomous nervous system, specifically pulse rate variability, and electrodermal activity. Additionally, we integrate data from a cost-effective eye-tracker. Our machine learning algorithms identify ’hotspots’ within the content and regions corresponding to a high cognitive load. These hotspots represent real-time predictors of comprehension difficulties. By integrating physiological data with contextual information (such as the levels of experience of individuals), our approach achieves an accuracy of 72.11% ± 2.21, a precision of 0.77, a recall of 0.70, and an f1 score of 0.73. This study opens possibilities for developing intelligent, cognitive-aware interfaces. Such interfaces can provide immediate contextual support, mitigating comprehension challenges within content. Whether through translation, content generation, or content summarization using available Large Language Models, this approach has the potential to enhance language comprehension.