Estimating long-term trends in ecological communities requires that we have some model of how organisms relate to changes in environmental factors such as temperature, precipitation, and land use. Experimental approaches to develop these estimates are often cost-prohibitive or are logistically impractical. As a result, a large and active literature has arisen that attempts to model the suitability of habitat for species and communities based on statistical analysis of current patterns of their occurrence and co-occurrence at large geographic scales. Despite being instrumental to many real-world decisions, these models are accompanied by many sources of uncertainty that are often ignored or poorly communicated. In this chapter, we focus on a subset of these methods, called “species distribution models,” to highlight some of the key uncertainties that arise when modeling ecological processes from occurrence data.