Temperature and salinity often define the distributions of aquatic organisms. This is at least partially true for Delta Smelt, an imperiled species endemic to the upper San Francisco Estuary. While much is known about the tolerances and distribution of Delta Smelt in relation to these parameters, little is known regarding the temperature and salinity preferences of the species. Therefore, the temperature and salinity preferences of sub-adult Delta Smelt were investigated across a wide range of thermal (8-28 °C) and salinity (0-23 ppt) conditions. Replicates of ten fish were allowed to swim between two circular chambers with different temperature or salinity, and the distribution of fish between the chambers was recorded. We found that Delta Smelt showed no temperature preference below 15 °C, a modest aversion to the warmer tank from 15 to 28 °C, and a strong aversion to the warmer tank with elevated mortality at temperatures above 28 °C. Delta Smelt also preferred lower salinities, and this preference became more pronounced as salinity increased toward 23 ppt. These results indicate that Delta Smelt can tolerate high temperatures and salinities for a short time, and that their preferences for lower temperature and salinity strengthens as these variables increase.