Desert springs are critical for wildlife and human subsistence, but poorly studied. The springs in the northern Chihuahuan Desert region of Mexico are no exception. While groundwater overexploitation and other anthropogenic activities have endangered these waters, little is known about their water quality or biodiversity. We monitored five springs on a monthly basis for one year, and two others sporadically, to determine their physicochemical characteristics and to study rotifer community composition as an assessment of biodiversity. Seasonal variation in temperature, dissolved oxygen (DO), and conductivity was observed in the five springs. DO was occasionally below the criterion for aquatic life (<4mg/L) in some springs. Ca2+ (468-775.2 mg/L) was the dominant ion in all springs except Ojo de Santa María where Na+ (180-290 mg/L) dominated. Of 57 rotifer species identified, Lepadella patella (Müller, 1786), Lepadella triptera (Ehrenberg, 1830), and Philodina megalotrocha, Ehrenberg, 1832 were present in most springs. The rotifer community exhibited nestedness among the sites (supported by four null modes, p<0.05) and was correlated with fall season, DO, and nitrate concentration. This work provides information that will aid in management practices and provide important baseline data on water quality and regional diversity of a major component of the zooplankton.