Desert wetlands, in particular those slow moving bodies of water known as cienegas, are important sites for biodiversity in arid landscapes and serve as indicators of hydrological functioning on the landscape-level. One of the most extensive systems of cienegas, historical or extant, in southeastern Arizona lies along Cienega Creek, located southeast of Tucson, Arizona. Satellite imagery analysis is heavily utilized to determine landscape-level trends, but cienegas present a challenge to traditional analysis methods. The Normalized Difference Vegetation Index (NDVI), the classic measure of vegetation greenness, reacts counter-intuitively to open water and is affected by open ground, both common occurrences in cienega habitats. Additional remote sensing indices have been developed that balance sensitivity to these environmental elements. This research explores these remote sensing indices at Cienega Creek applying one topographic index to current elevation data and five spectral indices to Thematic Mapper imagery from 1984 to 2011. Temporal trends were identified for all spectral indices and all indices were compared for suitability in cienega habitats. Temporal trends were analyzed for spatial clustering and spatial trends identified. The Normalized Difference Infrared Index utilizing Landsat Thematic Mapper band 5 outperformed other indices at differentiating between cienega, riparian, and upland habitats and is more suitable than NDVI for analyzing cienega habitats in such circumstances.