The natural processes taking place in coastal zones—such as erosion, sea level rise, and alien species invasion—combined with increasing anthropogenic pressure, have significantly affected the population of Pancratium maritimum in Greece. This is particularly evident in regions like northwestern Crete, where the dual identity of intense tourist development and ecological significance creates a challenging management landscape. The present study focuses on a 22 km stretch of the NW coastline of Chania, a part of Crete that not only includes Natura 2000 protected areas but also exemplifies the island’s role as a tourism hotspot, contributing directly to 33% of Greece’s tourism GDP. Sampling involved recording the presence and abundance of the species, as well as soil parameters such as soil moisture, temperature, pH, and intervention factors (irrigation, fencing, pollution, existence of umbrellas). Principal component analysis (PCA) revealed two distinct axes of pressure. The first Principal Axis, PC1 was mainly associated with anthropogenic parameters, while PC2 was mainly associated with natural/environmental factors ( soil moisture, temperature, and pH). Through the visualization of heat maps of PC1 and PC2, sections of the coastline with intense anthropogenic pressures were highlighted, as well as areas with more natural, favorable dynamics for the presence of the plant. Classification through k-means clustering grouped the study points into three categories depending on the pressure profiles. Finally, a GLM (Quasi-Poisson) model highlighted soil temperature as the most important factor that negatively affects the presence of Pancratium maritimum. The findings underscore the importance of targeted coastal ecosystem management tailored to the ecological needs of priority species, particularly in high pressure areas where economic and environmental interests intersect.