We used occupancy modeling to investigate habitat use by White Sands pupfish (Cyprinodon tularosa) in a 53.4-ha ciénega supported by discharge from Malpais Spring. The ciénega has been subject to considerable alteration by humans over the last ca. 200 years, resulting in dynamic conditions of emergent wetland vegetation structure and composition and spatial variation in surface water characteristics. Site occupancy models were developed to describe variation in probabilities of detection and habitat use. Detection of White Sands pupfish was negatively influenced by total emergent wetland plant cover, and less so by survey-specific measurements of water temperature and cloud cover. Site occupancy, which we interpreted as habitat use because we did not assume site closure, was consistently influenced by additive effects of water depth and cover by beaked spike-rush (Eleocharis rostellata) in top-ranked models. In the top-ranked model, with other covariates set at their mean value, habitat use probability reached a plateau at 1 at a water depth of ≥30 cm, and habitat use probability fell below about 0.6 when beaked spike-rush cover was ≥0.7. The top-ranked models indicated that habitat use was also influenced to a lesser extent by chairmaker's bulrush (Schoenoplectus americanus) cover and floating algal mats. The negative effect of chairmaker's bulrush cover on habitat use probability was moderated by water depth. Application of depth and spike-rush cover criteria taken from the top-ranked model produced an estimate of 1.58 ha of high-use probability habitat in the ciénega. The results have implications for monitoring the pupfish population and its habitat, and for development of reference conditions for management of the Malpais Spring ciénega.