The tropical dry forests of NW Peru are heavily shaped by the El Niño Southern Oscillation (ENSO), where especially El Niño brings rain to arid to semi-arid areas. However, the resulting effects on biodiversity patterns remain largely unknown as well as the effect of environmental variables on the floristic composition under varying rainfall patterns. Therefore, we studied the spatio-temporal effects of different ENSO episodes on floristic biodiversity along a climatic gradient ranging from the coastal desert to the Andean foothills. We sampled 50 vegetation plots in four years representing different ENSO episodes. To highlight the spatio-temporal changes in floristic composition and beta diversity across ENSO episodes, we predicted ordination scores with a Generalized Additive Model. We applied variation partitioning to test if topographic or edaphic variables gained in importance during more humid ENSO episodes. Additionally, we executed an irrigation–fertilization experiment to quantify the beneficial effects of the water–nutrient interaction under different simulated ENSO rainfall scenarios. Plant species richness increased under humid conditions during the humid La Niña (2012) and the moderate El Niño (2016), and slightly decreased under the very humid conditions during the coastal El Niño (2017). The spatial prediction revealed that specific vegetation formations became more pronounced with increasing water input, but that a large water surplus led to the disruption of the strict order along the climatic gradient. Edaphic and topographic variables gained in importance with increased water availability (2012 and 2016), however, this effect was not further amplified under very wet conditions (2017). The experiment showed that plant cover under Super Niño conditions was three times higher when fertilized. Overall, our spatial predictions concede detailed insights into spatio-temporal ecosystem dynamics in response to varying rainfall caused by different ENSO episodes while the results of the experiment can support farmers regarding a sustainable agrarian management.