The state of a population of planktic foraminifers at a certain time reflects multiple processes in the upper ocean, including environmental conditions to which the population was exposed during its growth, the age of the cohorts, and spatiotemporal patchiness. We carried out depth-stratified (0–60, 60–100 m) replicated sampling off Puerto Rico in autumn 2012, revisiting three stations previously sampled in autumn 1994 and spring 1995, in order to analyze seasonal and interannual variability of planktic foraminifers and the stable isotopic composition of their tests. The merged dataset from all three sampling campaigns allows us to assess short- and long-term changes in foraminiferal population dynamics and the spatial assemblage coherency along the shelf edge. All three sample series cover more than 2 weeks during either spring (1995) or autumn (1994, 2012) and include the time of the full moon when reproduction of some surface-dwelling planktic foraminifers has been postulated to take place. Our analyses indicate that interannual variability affected the faunal composition, and both autumn assemblages were characterized by oligotrophic tropical species, dominated by Trilobatus sacculifer and Globigerinoides ruber (white and pink variety). However, G. ruber (white) had a higher abundance in 1994 (37 %) than in 2012 (3.5 %), which may be partially due to increasing sea surface temperatures since the 1990s. Between 60 and 100 m water depth, a different faunal composition with a specific stable oxygen isotope signature provides evidence for the presence of the Subtropical Underwater at the sampling site. Measurements on T. sacculifer sampled in autumn 2012 revealed that test size, calcification and incidence of sac-like chambers continued to increase after full moon, and thus no relation to the synodic lunar reproduction cycle was recognized. During autumn 2012, outer bands of hurricane Sandy passed the Greater Antilles and likely affected the foraminifers. Lower standing stocks of living planktic foraminifers and lower stable carbon isotope values from individuals collected in the mixed layer likely indicate the response to increased rainfall and turbidity in the wake of the hurricane.