Rhythmography and omegametry have been used to study the physiological functions in 45 sailors during a 157-day sea voyage in the northern and northwestern Atlantic. The characteristics of the formation of compensatory and adaptive responses of sailors to long-term, chronic stress caused by work at sea are analyzed. Patterns of the variation in autonomic tone in different months of the long voyage and the dependence of the constant potential of the brain on the autonomic balance are described. Markov chain models are used to simulate the adaptation outcome for different states of the autonomic balance. The specific features of the functional physiological characteristics of sailors at different levels of functional reactivity are analyzed. It is found that humoral mechanisms serve as a link between the factors ensuring structural and functional rearrangement of the mechanisms of constant potential formation in chronic fatigue. A reciprocal mechanism is shown to underlie the formation of functional states during the second half of the voyage.