Environmental variation in space and time are key drivers of phenotypic and genetic diversification of natural populations, but the role of space - time interactions as well as the underlying mechanisms of diversification (e.g. phenotypic plasticity versus direct genetic and parental effects) - are still poorly understood. Lake Myvatn threespine stickleback (Gasterosteus aculeatus) offer a rare opportunity to study early stages of diversification due to the young age and known spatial (e.g. temperature and biota) and temporal (e.g. strong fluctuations in the abundance of chironomid midges) environmental heterogeneity of the lake. We studied Myvatn stickleback across five habitat types and four consecutive years (2009 to 2012) to investigate the relative importance of space and time as drivers of phenotypic diversity in this system. We found clear temporal phenotypic changes, but also consistent phenotypic differences (i.e. body size, defense and feeding morphology) and subtle population genetic divergence across some of the habitats. We discuss the putative key drivers of diversification of Myvatn stickleback and the general implications of our findings for diversification in dynamic natural systems.