This study investigates the indirect effects of primary productivity enhancement via fertilization, and the direct effects of environmental differences at two elevations, on the density and species richness of leaf-litter spiders. Litter was sampled in tabonuco forest (340–360 m elevation) and elfin forest (1051 m elevation) within the Luquillo Experimental Forest Long Term Ecological Research (LTER) site in Puerto Rico. Treatments consisted of three blocks with fertilization and control plots at both sites, and a one time removal of hurricane generated debris at tabonuco forest only. Treatments had no significant effect on spider density, species diversity, and species richness at either elevation. Elfin forest showed lower densities and lower species richness than tabonuco forest due to harsh environmental conditions. The thin litter layer and similar standing litter in the tabonuco forest suggest that spiders are limited by habitat, and also that they have successfully recolonized the debris cleared areas at this elevation. Harsh environmental conditions at elfin forest seem to be strong enough to counteract the effects of fertilizer addition on the measured variables. However, the high biomass of grasses in the fertilization plots at elfin forest could have caused an underestimation of spider densities. This study suggests that habitat availability is an important variable in bottom-up models for food web link control.