Karst systems have a high degree of heterogeneity and anisotropy, which makes them behave very differently from other aquifers. Slow seepage through the rock matrix and fast flow through conduits and fractures result in a high variation in spring response to precipitation events. Contaminant storage occurs in the rock matrix and epikarst, but contaminant transport occurs mostly along preferential pathways that are typically inaccessible locations, which makes modeling of karst systems challenging. Computer models for understanding and predicting hydraulics and contaminant transport in aquifers make assumptions about the distribution and hydraulic properties of geologic features that may not always apply to karst aquifers. This paper reviews the basic concepts, mathematical descriptions, and modeling approaches for karst systems. The North Coast Limestone aquifer system of Puerto Rico (USA) is introduced as a case study to illustrate and discuss the application of groundwater models in karst aquifer systems to evaluate aquifer contamination.