The white-cheeked pintail (Anas bahamensis) is listed as threatened, and survey data are needed to assess population status, estimate trends, and guide management on Puerto Rico and territorial islands. We surveyed 51 points in 29 wetland sites to estimate density and population size after the peak of reproduction (Mar–Jul) and before the waterfowl hunting season (Nov–Jan). Estimated density was 2.33 individuals/ha (SE = 0.27), and estimated population size was 3,755 individuals (SE = 435, log-normal 95% CI = 2,995 to 4,708) in 1,614 ha surveyed in August–October 2003–2005. Density differed between August–October 2003 (𝐷̂ = 3.07 individuals/ha, SE = 0.41) and 2004 (𝐷̂ = 1.26 individuals/ha, SE = 0.17) and between August–October 2004 and 2005 (𝐷̂ = 2.54 individuals/ha, SE = 0.47) but not between August–October 2003 and 2005. Spatial distribution ranged from nearly random (estimate of dispersion parameter [𝑏̂] = 0.99) to highly clumped (𝑏̂ = 3.71). We suggest that spatiotemporal variation of wetland hydrochemical conditions caused changes in foraging resources, which in turn caused changes in white-cheeked pintail density and spacing patterns. We recommend surveying 186 points 3 times in August–October for estimated density to have a coefficient of variation of 0.10, even when white-cheeked pintails are highly clustered (estimate of exp cluster size, Ê[s] = 16.1, SE = 2.8) and clumped (b = 4) in space. We provide additional recommendations for integrating monitoring, research, and management objectives to better understand the ecology and promote the conservation of white-cheeked pintails and their habitats locally and regionally.