The Bonne Femme watershed, located in central Missouri, is a rapidly urbanizing area, and this study was undertaken to characterize the hydrology of two karst aquifers within this watershed before significant increases in impervious surface occur. The objectives of this study were to: 1) delineate the recharge areas for Hunters Cave (HC) and Devils Icebox (DI) cave; 2) quantify stream discharge at the resurgence of HC and DI caves; and 3) characterize the chemical and physical status of the cave streams. The quantity and quality of the water at the resurgence of both cave streams was monitored from April 1999 to March 2002. Both recharge areas were determined to be of similar size (33.3 km² for HC and 34.0 km² for DI) and were formed in the same geologic strata. Average annual discharge was 1,900,000 m³ at DI and 1,170,000 m³ at HC. Average monthly discharge was 97,700 m³ at HC and 158,000 m³ at DI. However, median instantaneous discharge over the three years was 18% higher at HC (74 m³/h) compared to DI (63 m³/h). Turbidity and pH showed the largest differences between sites, reflecting the greater magnitude and duration of runoff events and the higher row-cropping intensity in the DI recharge area. The HC recharge area is characterized by limited sub-surface conduit development, small conduits, short flow paths from surface to resurgence, and predominantly allogenic recharge. The DI recharge area is characterized by extensive sub-surface conduit development, large conduits, long flow paths to the resurgence, and both autogenic and allogenic recharge.