The karst-dominated Lower Suwannee River Basin (LSRB) spans several Florida counties where agricultural activities have potential to affect the groundwater, springs, and estuary. Data show vertical movement of P in soils, but a common assumption is that P transport is restricted once it reaches limestone. This assumption need not be true since P-enriched water may not have sufficient contact time with the limestone to be retained by the rock. Previous research has indicated that there is a delay time between P loading from an agricultural source and the movement of the P to a water body. A concern is that once P reaches an outlet (e.g., spring), elevated P concentrations could persist for years even if P applications were discontinued. A GIS approach is being used to determine if there is a significant elevation of P in springs nearest to agricultural sources. Another issue for the LSRB is allocating the contributions of agricultural P and natural P from phosphatic geologic formations and soils upstream from the karst region of the Basin. Water quality data for river, tributaries, springs, and estuary reveal total P concentrations (mostly dissolved) of up to several mg L^-1 in tributaries of phosphatic watersheds. Do agricultural P inputs pose a significant ecological risk to the estuary in light of the natural P loading? This is a challenging question yet to be resolved.