In wild populations natural selection is a constant companion and adaptation the only way of surviving, and in the long-term that adaptation must be heritable. Daphnia represent an ideal system to test for heritable adaptation as they are a widespread freshwater zooplankton. Even though different species are found all over the world, individual populations have limited dispersal ability and are mostly confined to their lake and compelled to adapt to that lake’s properties and its fluctuations. Daphnia reproduce mainly asexually, but when presented with adverse environments they produce resting eggs which can be recovered from lake sediments. These eggs can be hatched in the laboratory and provide snapshots of past phenotypes and genotypes. Switzerland’s lake Greifensee has been intensively studied over the past decades during which time the environment within the lake changed a lot. In the second half of the 20th century human-caused eutrophication of the lake took place, peaking in the 1950-1970s and a subsequent clearing of the lake water when waste water treatment plants were put into operation. By using the resurrection method, it has previously been shown that Daphnia from times of eutrophication are better adapted to pollution in water than their counterparts originating from times of clear water. In this Thesis, I combine whole genome resequencing and population genetic methods to find genetic evidence of this adaptation in 43 Daphnia galeata clones hatched from ephippia taken from dated core samples of Greifensee originating from 1958 to 2012. The population genomic methods I used revealed genetic differentiation and isolation over time, temporal population structure and evidence of strong diversifying selection. Comparison of allele frequencies with long term environmental data collected from Greifensee, suggests a strong association between allele frequency and environmental parameters particularly phosphorous and temperature. My results identify a number of variable sites in the Daphnia galeata genome that are correlated with changing environments, and these candidates can be used in future studies to test functional significance. In the final section of my thesis I also discuss the many technical advances in Daphnia growing and harvesting that was made during this research.