The proximate and ultimate mechanisms behind individual behavioural phenotypes are still only partially understood, with studies often focusing on a single or a few factor(s) that affect behaviour in a controlled environment. To understand the development and consequences of individual behavioural phenotypes in their complexity, a comprehensive approach is needed that analyses the effects of a broad spectrum of factors and their interactions on behaviour within the natural environment. We used focal observations to quantify four key behavioural components of Galápagos sea lion, Zalophus wollebaeki, pups under natural conditions: general social interactions, swimming, resting and social play behaviour. We then investigated the influence and interplay of age, sex, body condition, basal cortisol and testosterone levels, personality scores and the social environment on the observed behaviour. We identified significant correlations between all measured factors and behaviour. Complex interactions between testosterone, boldness and social play especially stand out, with the effect of boldness on social play being dependent on testosterone levels. We also demonstrate the importance of the early social environment, defined as local population density, for social play and, interestingly, time spent swimming. This could have consequences for the development of social and hunting skills, crucial for later stages of ontogeny. For this endangered pinniped, a decline in the diversity of social environments due to dwindling population numbers could lead to a decline in behavioural diversity and lower coping abilities towards future changes in their environment. Our study reveals important factors for the development of individual behavioural phenotypes of young Galápagos sea lions and elucidates some aspects of the architecture behind this individual variation in behaviour.