Objectives: This study characterised mental health, motivation, and their interrelations among 38 elite student athletes over a 13-week season, while monitoring and considering the influence of their athletic and academic schedules.Design: Longitudinal.Method: Electronically-administered questionnaires measured total mood disturbance and depressive symptoms (weekly), sleep quality and trait anxiety (monthly), and motivation, basic needs satisfaction and motivational climate (weeks one and 13).Results: Thirty-seven percent of athletes reported scores indicative of mild-to-moderate depression, 32% were poor sleepers, and 8% were high trait anxious. These outcomes significantly improved over time, whereas the motivation-related variables remained stable. The athletes were predominantly intrinsically motivated, and reported high satisfaction of basic psychological needs. Task climate exceeded its ego counterpart. There were no significant sex-related differences for any mental health outcome at week one; however, autonomy and relatedness were significantly higher among females.Conclusions: Collectively, these findings suggest that psychological monitoring of student-athletes, particularly over intense athletic and academic periods, is a powerful tool for identifying potential mental health and/or motivation-related issues that may influence performance and well-being.