We report the design and application of MEMS temperature and electrical conductivity sensor arrays for studying the harsh environments of hot springs. Centimeter-scale measurements were necessary to measure geochemical gradients across photosynthetic bacteria transition zones. Platinum, Parylene-C, and fused silica were critical materials used in fabrication. More than 700 temperature and 90 conductivity measurements were taken in the mixing zone where two geochemically different hot spring channels converged and the data show that the temperature gradients play an important role in determining where photosynthetic organisms appear. Additionally, a novel technique was developed for studying conservative parameters at centimeter spatial scales.