Habitat stability is an important factor that strongly influences individuals and their interactions. Both the stability of a habitat and the most prevalent conditions in it can determine ecology and phenotype of individuals that inhabit it. This should be reflected by both the niche they occupy in the habitat and their phenotype. There is still a lack of studies showing causes and effects of individual specialization on individual and population niches. To study the influence of habitat stability on these factors, I analyzed the individual diets of and conducted phenotypic analyses on trout from environmentally stable groundwater fed and unstable surface water fed streams in the Lake Lucerne drainage. There were clear ecological differences between stream types. Individuals from the stable habitat showed a higher degree of specialization than those from unstable habitats. The population niche in the stable habitat, hence, consisted of many smaller, specialized individual niches, with most of the variation in the between-individual component. In the unstable habitat, it consisted of overlapping, generalist niches with a high within-individual component to variation. Overall, my study showed that habitat stability can be an important factor in determining the niche of individuals in the habitat. I also used microsatellites to show that each stream could be considered a separate replicate. I found statistically significant differences in phenotype, both color and shape.