Diatoms are microscopic, single-celled algae living in almost all moist and aquatic environments with sufficient light. Recently, diatoms living on soils have been explored as tracers of water flow-paths during rainfall-runoff events. Although the results were promising, further use was hampered by the lack of knowledge on the ecology of those diatoms and the large number of samples needed. To overcome both obstacles, the spatial and temporal dynamics of diatom communities and their abundances on soils were investigated and tested against an extensive set of environmental variables. Also, in order to decrease the number of samples, a suspended sediment sampler was explored for sampling diatoms in streams. Our results allow to reduce the sampling effort and speed up the analysis of diatom-based hydrological tracer studies. They also indicate that more locations can be sampled and that the number of stream sampling sites can be increased in the future.