The state of conservation biology is most often defined in terms of what is known about terrestrial ecosystems. Contrary to what can sometimes be read in that literature, the largest stumbling block on the way to successful biodiversity management and conservation in aquatic ecosystems is the lack of quantitative baseline data, and the associated ignorance about diversity under the water surface. In the absence of data, goals are often set as qualitatively defined “reference conditions”, an approach that can be subjective, that risks broad brush generalisation and suffers from the shifting baseline syndrome. To combat these issues we launched several large integrated biodiversity mapping efforts for fish in Switzerland, Projet Lac in 2010, and more recently Progetto Fiumi. Our second focus is on the population genetics and ecology of invasion and range expansion on the one hand, and decline and extinction on the other. Here we study Threespined stickleback at the invasion front north of the Alps and at the extinction front south of the Alps.