Stable isotopes in the water molecule (2H or D and 18O), carbon, and nitrogen are useful tracers and integrators of processes in plant ecohydrological systems across scales. Over the last few years, there has been growing interest in regional to continental scale synthesis of stable isotope data with a view to elucidating biogeochemical and ecohydrological patterns. Published datasets from the humid tropics, however, are limited. To be able to contribute to bridging the “data gap” in the humid tropics, here, we publish a relatively novel and unique suite of δ13C, δ15N, δ2H, and δ18O isotope data from three sites across a moisture gradient and contrasting land use in Puerto Rico. Plant tissue (xylem and leaf) samples from two species of mahogany (Swietenia macrophylla and Swietenia mahagoni) and soil samples down to 60 cm in the soil profile were collected in relatively “wet” (July 2012) and “dry” (February 2013) periods at two sites in northeastern (Luquillo) and southwestern (Susua) Puerto Rico. The same sampling suite is also being made available from a highly urbanized site in the capital San Juan. Leaf samples taken in July 2012 and February 2013 were analyzed for δ13C and δ15N; all xylem and bulk soil samples were analyzed for δ2H and δ18O. Soil samples taken in July 2012 were analyzed for δ13C and δ15N. Leaf δ15N and δ13C dataset showed patterns that are possibly associated with site differences. While spatial patterns were also apparent in soil δ15N and δ13C dataset, the positively linear δ15N –δ13C relationship tends to weaken with site moisture. Soil depth and site moisture patterns were also observed in the δ2H and δ18O datasets of bulk soil and xylem samples. The purpose of these datasets is to provide baseline information on soil–plant water (δ2H and δ18O, N = 319), δ13C (N = 272), and δ15N (N = 269) that may be useful in a wide range of research questions from ecohydrological relations to biogeochemical patterns in soils and vegetation.