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Classical models of structured populations do not apply well to species leaving in semilinear habitats such as freshwater fishes, since these habitats are intermediate between one-dimensional and two-dimensional stepping-stone models. In order to investigate the genetic diversity of such populations, we have developed a new simulation program called aquasplatche. It starts by dividing a user-defined vectorized network into segments of arbitrary length, each segment hosting a single deme. The program then proceeds by simulating the colonization of the environment from an arbitrary source, recording the evolution of the deme densities and the migration events between adjacent demes over time. This demographic history is then used to generate genetic data of population samples located in various segments of the network, using a backward coalescent framework. Different versions of aquasplatche are freely available on http://cmpg.unibe.ch/software/aquasplatche.