Electrical conductivity (κ) measurements of natural waters are typically referenced to 25 °C (κ25) using standard temperature compensation factors (α). For acidic waters (pH < 4), this can result in a large κ25 error (δκ25). The more the sample temperature departs from 25 °C, the larger the potential δκ25. For pH < 4, the hydrogen ion transport number becomes substantial and its mode of transport is different from most other ions resulting in a different α. A new method for determining α as a function of pH and temperature is presented. Samples with varying amounts of H2SO4 and NaCl were used to develop the new α, which was then applied to 65 natural water samples including acid mine waters, geothermal waters, seawater, and stream waters. For each sample, the κ and pH were measured at several temperatures from 5 to 90 °C and κ25 was calculated. The δκ25 ranged from -11 to 9% for the new method as compared to -42 to 25% and -53 to 27% for the constant α (0.019) and ISO-7888 methods, respectively. The new method for determining α is a substantial improvement for acidic waters and performs as well as or better than the standard methods for circumneutral waters.