Vernal pools are unique ecosystems that are under great threat from urban and agricultural expansion. Many of the biological processes critical for successful construction and restoration of vernal pools, including those that allow fairy shrimp cysts to hatch, are not well understood. To further research on vernal pool functioning, we conducted a one-month study of two vernal pools on the Caltrans Mitigation site in Madera County, California. We placed data-logging temperature sensors along the long axis at the bottom of each vernal pool; over three site visits we also collected water quality data (temperature by a second method, pH, conductivity, and dissolved oxygen) at these same points. In addition, we collected data on aquatic community, pool morphology and hydrology, and rainfall on the site. Although other studies have recognized that direct precipitation infl uences the morphological characteristics of vernal pools in general, we found these two individual vernal pools to be quite different in both their morphology and hydrology in response to precipitation. One pool increased fi vefold in surface area and only gradually in depth, while the other pool increased 1.5-fold in depth while increasing, then decreasing in surface area over the study period. We found that the two pools support different aquatic communities, most likely based on these differences in habitat. Additionally, we found that a spatial temperature distribution existed in one vernal pool by analysis of variance (temperature sensors from second pool will be retrieved once pool dries). By regression analysis we found that “position” (distance from the pool edge along long axis) explains trends in temperature and pH better than “depth” (water level above each sensor, from pool bottom to surface). Conductivity and dissolved oxygen showed no signifi cant trends in regards to position or depth. The existence of microhabitats within a vernal pool may explain our fi ndings of spatial temperature stratifi cation and the stronger relationships between water chemistry variables and position (versus depth). There is ample support in the literature for microhabitats in lotic systems, whereas this is a new fi nding for vernal pools and as such, warrants further study especially as it relates to the ecology of natural and mitigated vernal pools