Nurses experience significant stress and emotional exhaustion, leading to burnout and fatigue. This study assessed how the nurses’ mood and fatigue evolves during their shifts, and the lagged and accumulated factors that influence these phenomena. A two-level design with repeated measures was applied to a sample of 113 nurses, performing an ecological momentary assessment of different parameters and multilevel longitudinal two-level modelling of the data. Accordingly, mood appeared to be explained by effort, by the negative lagged effect of reward and by accumulated effort, each following a quadratic trend, and it was influenced by previously executing a direct care task. By contrast, fatigue was explained by the current and lagged effect of effort, by the lagged effect of reward and by accumulated effort, again following quadratic trends. Fatigue was also associated with direct care, and the prior effect of documentation and communication tasks. Mood was also explained by problem-focused and emotion-focused coping strategies, indicative of negative mood, and by support-seeking and refusal coping strategies. Hence, mood and fatigue do not depend on a single factor like workload but rather, on the evolution and distribution of tasks, as well as on the stress during a shift and how it is handled.