Geology
Relief in the basin decreases westward, as the water flows east over the Cody Scarp onto the karst limestone plain. The eastern portion of the basin is underlain by over 100 feet of sands, clays, and carbonates that comprise the surface sediments and Hawthorn Group formations. This relatively high plateau region is termed the Northern Highlands. Land surface elevation decreases to the west exposing a limestone plain covered with a thin veneer of sands called the Western Valley.
It is in this area where groundwater in the Floridan aquifer or aquifer system flows out of the limestone aquifer via conduits as springs along the river. The Floridan aquifer in western Alachua County, southern Columbia and eastern Gilchrist counties is overlain by relatively thin undifferentiated sands. These porous sands permit high recharge and allow pollutants, such as nitrate, direct access to the Floridan aquifer. Karst conditions dominate the landscape in the western part of the basin, with sinkholes, springs, siphons (that take water back into the aquifer) and underwater caves present as common features.

River Basin
The Santa Fe River Basin encompasses 1,384 square miles in north Florida. The Santa Fe River extends from the headwater swamps of the Santa Fe River near Lake Santa Fe and Lake Alto to the confluence with the Suwannee River south of Branford. The basin includes the southern portions of Bradford, Union, Columbia and Suwannee counties and the northern portions of Alachua and Gilchrist counties. The Santa Fe River is a narrow river that has a forested corridor with natural communities ranging from bottomland hardwood swamps to mixed hardwood and pine uplands. The river has three major tributaries: Olustee Creek, the New River and the Itchetucknee River. The largest municipalities in the basin are High Springs in Alachua County and Fort White in Columbia County. The Santa Fe River Springs are located in the lower reaches of the Santa Fe River upstream of its confluence with the Suwannee River.
The Santa Fe River Basin and surrounding area has mixed land uses. The upper reaches of the watershed is agriculture, silviculture, and low density residential landuse. The lower reaches of the basin and adjoining areas is pasture, both improved and unimproved. As north Florida becomes more urbanized, residential land uses will likely increase.

Map disclaimer: some of the springs and swallets on this map may be locally known by other names.

Springs
The majority of the springs contributing water to the river are located downstream of Santa Fe River Sink and Rise, the rise itself being a first magnitude spring. This physiographic area is known as the High Springs Gap, and is a transition area from the Northern Highlands to the Western Valley limestone plain of the coastal lowlands. Most of the springs are located in Alachua, Columbia, Gilchrist, and Suwannee counties. Along the Santa Fe River downstream of Santa Fe River Rise and upstream of Cow Creek, there are 36 springs and 10 siphons. Many additional springs, sinks, and swallets are concentrated in the Itchetucknee River basin, along the Columbia and Suwannee county lines. A swallet is a closed depression or sinkhole into which all or part of a stream or river disappears underground. During periods of low flow, spring flow discharging from the Floridan Aquifer dominates flow in the lower portion of the Santa Fe River and water clarity in the river is high.