The discrete nature of vernal pools provides opportunities for experiments revealing information applicable to numerous habitats otherwise more difficult to examine in their entirety. This study examines vernal pool diversity in relation to pool thermal regime, morphology, and inter-pool distribution. Using Island Biogeography theory, we predicted that (1) the number of species in a community should be positively correlated with habitat size, and (2) inter-pool distance should be negatively correlated with biological similarity. We developed two alternative hypotheses, based on the expectation that larger pools should be more thermally stable. These hypotheses ask whether thermally stable or variable pools facilitate invertebrate diversity. We studied eight vernal pools on Kennedy Table in Madera County, California. We took measurements of surface-area, mean depth, and volume of each pool, temperature was logged for four weeks, and invertebrates were systematically sampled. All data was analyzed with Pearson correlation or stepwise multiple regression. The results indicated strong negative correlations between average depth with temperature maximum and temperature standard deviation. Pool proximity and invertebrate assemblage similarity were positively related. There was no significant correlation between temperature variation and species richness. Species diversity was not significantly correlated with pool morphology. Our study suggests that vernal pools do not follow standard theories about species diversity. As vernal pools diminish, it is increasingly important for similar studies to continue and expand in order to better understand the driving forces behind their unique faunal assemblages.