Eutrophication has long been known to negatively affect aquatic and terrestrial ecosystems worldwide. In freshwater ecosystems, excessive nutrient input results in a shift from vascular plant dominance to algal dominance, while the nutrient-species richness relationship is found to be unimodal. Eutrophication studies are usually conducted in continuously aquatic or terrestrial habitats, but it is unclear how these patterns may be altered by temporal heterogeneity driven by precipitation and temperature variation. The California vernal pool (CVP) ecosystem consists of three distinct phases (aquatic, terrestrial, and dry) caused by variation in climatic conditions. The purpose of this study was to test the hypothesis that resource addition during the aquatic phase results in increased algal abundance, which reduces vascular plant cover and richness of the terrestrial phase upon desiccation. We used mesocosms layered with CVP soil, in which treatments consisted of five levels of nitrogen and phosphorous added every 2 weeks. Resource addition increased available phosphorus levels and algae cover during the aquatic phase. Increased algal crusts resulted in decreased vascular plant percent cover and species richness. Few significant patterns were observed with individual plant species and total biomass. The phosphorus-plant richness relationship was not significant, but species composition was significantly different among the low and high treatment comparisons. These results highlight a neglected effect of eutrophication in seasonal habitats. Interactions among ecosystem phases clearly require more attention empirically and theoretically. Management and restoration of temporally heterogeneous habitat, such as the endemic-rich CVP, need to consider the extensive effects of increased nutrient input.