For the Mediterranean plant diversity hotspot, temporary pools combine a highly variable, rainfall-dependent habitat with high and endangered plant diversity within small surfaces. They show alternating phases of drought and flooding, corresponding to the characteristic summer drought and winter rain of Mediterranean climate. This alternation is coupled with a moisture gradient that behaves as a selective filter on vascular plants. The main aim of our study was to show how plant functional traits respond to this moisture gradient, to build a greater understanding of the underlying functional mechanisms, and to formulate assembly rules. Our data showed that the frequency of plants with smaller seeds, later onset of flowering and hydrophytes increased with increasing water levels. These relations were uncovered by controlling for site effects using a mixed model approach. We discuss how our data can provide a basis to understand the limiting factors for plants withhigh conservation value, and what management strategies can be adopted in the context of environmental change.