We quantified genetic variation for ecological relevant traits in the presence and the absence of fish chemicals of eleven Daphnia ambigua clones that were isolated from six interconnected ponds that differed in water transparency. In a cohort life table experiment, we tested whether genetic variation for a set of key life history traits was present among these clones. In addition the phototactic behaviour of these clones cultured in the presence and the absence of fish kairomones was quantified using a biotest. We detected a significant effect of fish kairomones on the phototactic behaviour and a highly significant genetic variation among clones for this trait in D. ambigua clones isolated from ponds in De Maten. Differences in size at maturity among D. ambigua clones in De Maten were highly significant, whereas differences in spina length among D. ambigua clones in De Maten were not significant. The presence of fish chemicals did not affect the studied life-history traits. We observed a significant positive relationship between average phototactic behaviour for each population and size at maturity both in the presence as in the absence of fish kairomones. Most of the genetic differences could be attributed to a clone isolated from one clearwater pond that is not directly connected to the remainder of the pond complex.