Up until the beginning of the previous millennium, threats to the environment were mostly local and hence less difficult to combat. In the early 21st century, a large human population and high and increasing demands of energy, food, and other resources have led to a global climate crisis affecting nearly all life on Earth, biodiversity, and human societies alike. How will such a dramatic environmental shift affect the ecosystems? The Baltic Sea ecosystem is an interesting example in this respect, as it includes a dramatic environmental shift, starting from a freshwater lake but 8,000 years ago turning into a marine (brackish) sea with initially somewhat higher salinity than in the early 21st century. Marine populations of species that colonized the brackish water basin had to tolerate or adapt to one third their original salinity, lower density of the water, no regular tides, winter ice, and generally colder waters. Overall, these were dramatic environmental changes of magnitudes and rates of change similar to what is predicted from contemporary global environmental changes, including climate change. Indeed, the Baltic Sea is a “Darwinian laboratory” that can be explored to understand the role of plasticity, genetic variation, genetic structure and architecture, and demography using the sharp footprints of both phenotypic and genetic changes of organisms that survived this rapid environmental shift. What is observed is firstly that many marine species outside did not make it into the Baltic Sea, but among those that were successful, almost all (among the >30 studied macrospecies) show large genetic changes due to genetic drift and directional selection. The latter show that adaptation to a strong environmental shift is possible over a relatively short period of time for some species. Among successful survivors were species with very large population sizes and thus large standing genetic variation. In some species, hybridization contributed to increased levels of genetic variation. Only very few macroscopic species show evidence of recent adaptation following new mutations, while this was common among microbes. Reduced rates of recombination among genes through chromosomal inversions enable local adaptation, and it certainly supported the establishment of at least a handful of Baltic populations of species. Cloning, is also overrepresented among Baltic populations, and there may be several reasons for this. Cloning conserves suitable genotypes in marginal environments, and it also supports efficient range expansion in species that under sexual reproduction would require two individuals (one female and one male) to arrive close together after migration into a new spot. Being in an enclosed sea, the Baltic populations of largely cold water–adapted species are now facing the next large challenge—a much more rapid warming than elsewhere in the oceans.