Concerns exist that the degradation of water quality in Salado Creek near Salado, Texas could adversely affect recreational uses and harm salamander populations that live in and near springs that discharge into the stream. Salado is part of the rapidly growing Killeen-Temple-Fort Hood area; land-use changes in the Salado Creek watershed could adversely affect water quality in Salado Creek. Streamflow in Salado Creek is generally derived from the Salado Springs complex during low-flow conditions (dry weather) and from the springs and surface runoff during high-flow conditions (wet weather). A better understanding of the types of waste (human, animal, or both) that may be entering the stream and springs is needed to properly manage fecal-waste input. Water-quality samples were collected from four sites in Salado Creek near Salado over a variety of hydrologic conditions between May and September 2018. The samples were analyzed for nutrients, bacteria, and microbial source tracking markers. Known-source samples were collected from a wastewater plant, septic tanks, and animal droppings in the watershed. The known-source samples were analyzed for bacteria and microbial source tracking markers to characterize the types of waste in the watershed and compare them to the water-quality samples. Salado transitioned from on-site sewage facilities (septic tanks) to a municipal wastewater treatment system in some areas between 2014 and 2019. These results may help water resource managers assess the effects of the wastewater treatment system and other land-use changes in the area on water quality in Salado Creek and the Salado Springs complex.