Karst aquifers are vital sources of groundwater for domestic and industrial use in many parts of the world. To sustain rising population throughout the southeastern United States, karst aquifers are increasingly exploited to provide the populace a clean and reliable water resource. The moldic Spring Garden Member of the Castle Hayne Limestone and the vuggy Miami Limestone Formation of the Biscayne aquifer systems are two highly productive karst aquifers that provide critical water resources to millions of people in eastern North Carolina and southeastern Florida, respectively. In order to improve our understanding of karst media, a detailed investigation of 2D porosity and pore geometry of Castle Hayne and Biscayne aquifers was undertaken using image and geospatial analysis. The goal of this study was to compare and contrast the pore structure of moldic and vuggy karst aquifers by quantifying 2D porosity and pore geometry in borehole televiewer, slabbed core, and thin-section images. GIS provided an integrated environment for statistical and geospatial analysis, making it the ideal tool for identifying and extracting pore structures from the digital images. Macropore area and perimeter were derived from televiewer, core and thin-section images. These geometric attributes were used to calculate a shape measure. The shape measure provided additional insight into the potential for interconnectivity and geometry of pores across the multiple scales of observation. Results show that both pore area and perimeter for the Castle Hayne and Biscayne aquifers can be described by exponential distributions. The moldic Castle Hayne aquifer has larger pore perimeters, when similar pore areas are compared to those extracted from the vuggy Biscayne aquifer. The complexity of shapes are essentially identical at smaller scales of observation for pores derived from both the Castle Hayne and Biscayne aquifers. However, as the scale of observation increases, the difference between the pore geometries of macropores from the Castle Hayne and Biscayne aquifers also increases. At the two largest scales of observation, pores from the Castle Hayne are more complex than pores with identical areas from the Biscayne. Results also reveal that the scale of measurement plays a critical role in interpreting quantitative macropore structure within karst aquifers, thus requiring an approach that takes into account the scale of measurement of the macropore geometry. As scale of observation increases from thin-section to borehole image, pore size and pore complexity increase considerably over several orders of magnitude. Such quantitative measures can lead to a better understanding of porosity structure in karst aquifers that can be useful for designing and running groundwater flow models and assessing transport mechanisms in karst media. Most importantly, this study provides a quantitative assessment of the distribution of macropore geometry in karst aquifers with different structures and porosity.