This study examines the challenges Saudi university students face when using artificial intelligence applications in academic research, with particular attention to academic, cognitive-skill, and ethical dimensions. Adopting a quantitative descriptive survey design, the study collected data through an electronic questionnaire administered to 54 students at Imam Abdulrahman Bin Faisal University during November and December 2025. The findings reveal substantial challenges across all three dimensions. Academic challenges recorded an overall agreement rate of 73.9%, indicating concerns about weakened academic writing, reduced reliance on original sources, and limited independent problem-solving. Cognitive and skill-related challenges reached 67.6%, reflecting difficulties in selecting appropriate tools, distinguishing accurate from inaccurate outputs, and sustaining critical thinking. Ethical challenges were the most pronounced, with an agreement rate of 75.1%, especially regarding information accuracy, bias, proper citation, and responsibility for AI-generated errors. The study concludes that the growing use of AI in academic research requires structured training, clearer ethical guidelines, and balanced integration strategies that preserve students’ intellectual independence and research integrity within Saudi higher education.