Evolutionary ecology aims to better understand how ecologically important traits respond to environmental heterogeneity. Environments vary both naturally and as a result of human activities, and investigations that simultaneously consider how natural and human‐induced environmental variation affect diverse trait types grow increasingly important as human activities drive species endangerment. Here, we examined how habitat fragmentation and structural habitat complexity affect disparate trait types in Bahamas mosquitofish Gambusia hubbsi inhabiting tidal creeks. We tested a priori predictions for how these factors might influence exploratory behaviour, stress reactivity and brain anatomy. We examined approximately 350 adult Bahamas mosquitofish from seven tidal‐creek populations across Andros Island, The Bahamas that varied in both human‐caused fragmentation (three fragmented and four unfragmented) and natural habitat complexity (e.g. fivefold variation in rock habitat). Populations that had experienced severe human‐induced fragmentation, and thus restriction of tidal exchange from the ocean, exhibited greater exploration of a novel environment, stronger physiological stress responses to a mildly stressful event and smaller telencephala (relative to body size). These changes matched adaptive predictions based mostly on (a) reduced chronic predation risk and (b) decreased demands for navigating tidally dynamic habitats. Populations from sites with greater structural habitat complexity showed a higher propensity for exploration and a relatively larger optic tectum and cerebellum. These patterns matched adaptive predictions related to increased demands for navigating complex environments. Our findings demonstrate environmental variation, including recent anthropogenic impacts (<50 years), can significantly affect complex, ecologically important traits. Yet trait‐specific patterns may not be easily predicted, as we found strong support for only six of 12 predictions. Our results further highlight the utility of simultaneously quantifying multiple environmental factors—for example had we failed to account for habitat complexity, we would not have detected the effects of fragmentation on exploratory behaviours. These responses, and their ecological consequences, may be complex: rapid and adaptive phenotypic responses to anthropogenic impacts can facilitate persistence in human‐altered environments, but may come at a cost of population vulnerability if ecological restoration was to occur without consideration of the altered traits.