The study had two objectives: (a) to assess the prevalence of sleep-related habitability concerns in the berthing compartments of U.S. Navy surface ships and (b) to assess whether habitability issues in berthing compartments affected the sleep and well-being of crew members. The importance of habitability for human well-being is recognized. Little is known, however, about the association between habitability factors in the sleeping/berthing compartments and sailor well-being in operational conditions. Fit-for-duty sailors (N = 1,269; from six ships) participated in this naturalistic and longitudinal study. Sailors reported habitability factors affecting their sleep and completed four standardized questionnaires to assess daytime sleepiness, insomnia, sleep quality, and mood. Sleep was assessed through wrist-worn actigraphy and activity logs. Noise, ambient temperature, poor bedding conditions, and ambient light were the most frequently reported factors of concern. Compared to their peers with fewer complaints, sailors with more habitability-related complaints were more likely to have elevated daytime sleepiness (by 23%) and to report insomnia symptoms (145%) and lower sleep quality (21%). Sailors who reported more habitability-related issues also tended to sleep longer. Individuals with more complaints about habitability also tended to report worse mood (total mood disturbance, tension/anxiety, depression, fatigue, and confusion/bewilderment). Habitability-related complaints are associated with sailor well-being and sleep. Future studies should expound on the various detrimental factors that degrade conditions in berthing compartments and negatively impact crew well-being. Habitability in berthing compartments of surface ships is associated with sailors' daytime sleepiness, insomnia severity, mood, and sleep attributes. Ship designers should take these findings into consideration and investigate viable and cost-effective methods to mitigate the problems we identified.