FIG. 1: Location map of San Pedro geologic mapping. Blue and yellows boxes represent old and new AZGS mapping, respectively;  red boxes represent mapping by USGS or others.
Holocene mapping of the san pedro river system
a geologic approach to an environmental problem – water resource management
The Arizona Geological Survey (AZGS) Staff

The San Pedro River stretches from the mountains of north central Sonora, Mexico, across the semi-arid grasslands of southeast Arizona, to its confluence with the Gila River. It has two major tributaries – Babocomari River and Aravaipa Creek.

Arizona Courts and the San Pedro River Corridor

In September 2005, and as part of ADWR’s administrative and technical support to the adjudication court, Maricopa County Superior Court directed ADWR to determine the lateral limits of subflow in the San Pedro River watershed.  Because earlier court rulings held that the subflow zone is the zone of saturated floodplain Holocene alluvium, ADWR contracted AZGS – with its more than 20-years experience in Quaternary mapping – to provide consistent, detailed geologic maps of Holocene floodplain alluvium along more than 175 miles of the San Pedro River and its major tributaries – Aravaipa Creek and Babocomari River. For a more thorough discourse on the judicial history of “subflow”, and for a full description, see the Arizona Department of Water Resources (ADWR) report, Subflow Zone Delineation Report for the San Pedro River Watershed, June 2009.

In August 2009, the Arizona Geological Survey released six geologic map plates and a 76-page report focusing on Quaternary alluvium along a 2-mile swath centered on the San Pedro and Babocomari Rivers and Aravaipa Creek (Fig 1.) (Cook et al., 2009).   (Click here for PDF copies of the report and map)

San Pedro River System

The San Pedro River joins the Santa Cruz as one southeastern Arizona’s two major river systems.  From its headwaters in Sonora, Mexico, the San Pedro flows north about 140 miles, bridging the Chichuahuan and Sonoran Deserts, before joining the Gila River near Winkelman, Arizona.  It drains an area of nearly 4,720 sq. miles in Santa Cruz, Cochise, Graham, Pima, and Pinal Counties.  By convention, the San Pedro is subdivided into upper (southern) and lower (northern) reaches at the Narrows, a bedrock constriction north of Benson in Cochise County.

Along its northward course, the river flows through deep sedimentary basins flanked, from south to north, by the Huachuca, Mule, Whetstone, Dragoon, Rincon, Winchester, Galiuro, Santa Catalina and Tortilla Mountains.  All of these are north to northwest trending, fault-block mountain ranges formed during Basin and Range extension, roughly 25 to 5 million years ago.  Numerous ephemeral tributaries debouch into the San Pedro, but the two largest tributaries, the Babocomari River of Santa Cruz County and Aravaipa Creek of Graham County, have long perennial reaches.

The San Pedro attracted prehistoric and historic peoples.  About 13,000 years ago, ice age hunters – people of the Clovis culture – fanned across the San Pedro bottomlands hunting mammoth, horse, and bison (Amann, Jr, et. Al, 1998).  They were followed by later generations of Archaic hunter-gatherers, Hohokam and Apache.  The Tohono O’odham, Hopi, Zuni, and San Carlos Apache all lay claim to the San Pedro Valley as an ancestral home (Ferguson and Colwell-Chanthaphonh, 2006).

Since the 1870s, the San Pedro valley has been home to small communities engaged in cattle ranching, mining, agriculture, and more recently, tourism.  The valley bottomland changed dramatically as modification to the San Pedro River corridor – draining cienegas, constructing irrigation ditches, and building railroads and roads – modified the river floodplain, altered the riparian and valley ecology, and transformed the San Pedro River from a low-energy, broadly meandering stream into a higher energy, entrenched watercourse with a deeply incised channel. Natural factors may have also contributed to entrenchment.

Mapping Quaternary Alluvium

AZGS geoscientists used a six-stage process, outlined in Table 1, to map Holocene alluvium along the San Pedro River and its two major tributaries.  In brief, the geology of the river corridor was first scoped out and digitized on digital orthophotoquads and aerial photographs.  This was followed up with occupation of numerous field sites along the San Pedro and Babocomari Rivers and Aravaipa Creek to further delineate Holocene and Pleistocene river and piedmont deposits.  Wherever possible, formal observation waypoints comprising geologic descriptions and electronic photographs were established about one-mile apart along each of the three rivers.  These data were then downloaded into a GIS project to check the accuracy of map unit boundaries and to facilitate the accurate transfer of field data to the geodatabase.

We used standard geologic mapping criteria to differentiate Holocene river deposits from tributary deposits and older geologic units.  These criteria include drainage patterns, relative position in the landscape, surface color, vegetation assemblages, and soil development. We also consulted Soil Survey maps and archaeological sites that provided age constraints for river deposits.

Table 1.  AZGS Six-Stage Process of Mapping Holocene Alluvium in the San Pedro Drainage.
1. Compiling existing geologic data in ArcGIS – includes portions of 26 geologic maps, 18 of which are products of AZGS.
2. Re-examining existing maps using aerial photographs, 10-meter digital elevation models* (DEM), lidar-based topography, and traditional topographic analysis.
3. New mapping of Holocene alluvium where no large-scale mapping was previously available.
4. Field checking the boundaries of Holocene alluvium along the river – establishing GPS field stations on one-mile centers comprising ground photographs and detailed descriptions.
5. Revising map unit boundaries of extant geologic maps where necessary.
6. Constructing 1:24,000-scale geologic maps of a two-mile swath of the San Pedro and Babocomari Rivers, and Aravaipa Creek.
  *Ten-meter DEMs were provided by the US Geological Survey.

Chief Elements of AZGS Mapping

The two chief elements of AZGS mapping along the San Pedro, Aravaipa and Babocomari drainages were: 1) distinguishing alluvium and geomorphic features of the main trunk stream and its floodplain from that of tributaries; and, 2) fixing the extent, distribution, and relative ages of alluvium.

Fig. 2: Gently sloping floodplain of the San Pedro River.

Alluvial deposits of rivers are subdivided into two broad fields: channel sands and gravels, and overbank flood plain and terraces comprising sand, silt, and clay, with only minor gravel. A diverse assemblage of well-rounded pebbles and cobbles distinguish main trunk deposits from the lithologically monotonous, angular clasts complemented by a paucity of silts and clays of tributaries. Overbank deposits are characteristically fine-grained, but those of the main trunk tend to be more broadly distributed than those of the more physically confined tributaries.

Landform geometries provide another means for distinguishing between main trunk and tributary deposits: San Pedro River landforms – channel, flood plain, and adjacent Quaternary river terraces – are topographically subdued (i.e., low), with gentle slopes oriented in the down-valley direction of the modern river (Fig. 2; Cook et al. 2009). Tributary channels, flood plains, and terraces typically have steeper slopes oriented towards the axis of the valley.

Establishing a relative age sequence of Quaternary deposits

Dating young Quaternary-age sediments is a challenge.  Radiocarbon and cosmogenic dates are expensive and require fortuitous discovery of appropriate materials, and relative dating techniques – superposition, cross-cutting relationships, and original horizontality – provide stratigraphic control but fall short of delineating finely-calibrated chronologies.  To meet this challenge, Quaternary geologists in the desert Southwest have formulated a suite of empirical observations calibrated, whenever possible, by radiocarbon dates and archeological chronologies that permit Holocene-age deposits to be subdivided into modern, younger, middle and older deposits with some precision (Table 2).  The same observations applied to Pleistocene deposits yield credible results, albeit somewhat less calibrated and with a lower degree of accuracy.


Table 2.  Empirical observations and Archeological Data used in Time-Sequencing Quaternary deposits of the San Pedro River.

  • Color of Deposits.  Younger Holocene piedmont and river deposits – rich in silt, sand, pebbles and cobbles – are typically light to light brown in color; older Holocene deposits acquire a dark brown or slightly reddish hue.

    > Pleistocene deposits are somewhat redder as a result of clay accumulation and oxidation of near-surface soils, or lighter-colored because of the accumulation of calcium carbonate in soils.  Also, the presence of orange or black coated pebbles and cobbles on Pleistocene-age surfaces is equally diagnostic.

  • Morphology.  Holocene channel, sand and gravel bars, and swale deposits retain their formative morphology – shape, size and slope – to a great extent.  By inference, the more well-defined the morphology of the given feature, the younger it is. 

    > For Pleistocene deposits, the morphology of all but the youngest deposits are masked in part or entirely by erosion and deposition of sediments. 

  • FIG. 3: AZGS geoscientist aNN yOUBERG pointing to prehistoric rock-lined pit.
    Archaeological sites.  Over the past 13,000 years, the San Pedro River valley hosted populations of Clovis, Archaic, and Hohokam people – all of whom left their mark (Fig. 3; Cook et al., 2009).  The geoarchaeologist on our mapping team, Jill Onken, compiled previously reported and new chronological data – radiocarbon dates, projectile point and pot shard age-ranges – from 17 buried- and 37 surface-archaeological sites of two Holocene alluvium units: Qy2r and Qy3r.  As a result, the depositional period for unit Qy2r is particularly well-constrained to about 3500 – 1000 years before the present.  With Qy2r firmly anchored in time, inferences regarding the age of Qy1r – middle Holocene or older - are strengthened.
  • Landscape Position.  In its present incised condition, younger channel and terrace deposits are situated immediately adjacent to the river and at topographically lower positions than older, stranded terraces that are situated well above the river at 10s to 100s of meters from the present-day channel. 
  • Soil survey mapping.  Along the upper San Pedro River, soil survey mapping by the National Resources Conservation Service (NRCS) provided important control on Holocene- and Pleistocene-age estimates and proved particularly useful in bottomlands severely disturbed by agriculture, cattle ranching, or some other human activity. 


On San Pedro geologic maps, Holocene river alluvium is portrayed as active channel (Qycr) and flood channels, and low terraces and remnants of Holocene floodplains (from youngest to oldest: Qy4r – Qy1r) (Fig. 4; Cook et al., 2009). 

FIG. 4: Abridged geologic time scale for San Pedro Alluvium

As shown in Figure 5, bounding geologic units include: Holocene tributary alluvial fans and channels, Pleistocene alluvial fans and river terraces, eroded basin deposits, and bedrock.  We confined mapping to a two-mile swath for two reasons: 1) it fully encapsulates the lateral extent of Holocene river alluvium along the three drainages: and, 2) in all cases, a one-mile zone on each side of the drainage is sufficiently broad to encompass geologic bounding units – Holocene tributary alluvial fans and channels, Pleistocene alluvial fans and river terraces, eroded basin deposits, and bedrock. 

Extent of Holocene Alluvium along the San Pedro

The lateral extent of Holocene alluvium varies dramatically along the San Pedro and Babocomari Rivers and Arivaipa Creek.  In reaches where the streams cut through bedrock constrictions, alluvium may extend less than 100 ft to several hundred ft laterally from the active channel. 

Along the upper San Pedro River, this includes the northern part of the Lewis Springs quadrangle, parts of the Fairbank quadrangle, and the Narrows in the Wildhorse Mountain quadrangle.  For Aravaipa Creek, the entire Aravaipa Canyon reach is tightly constricted by bedrock ; as is much of the lower reach of the Babocomari River (Fig. 6).  In parts of the San Pedro River, alluvial fans constructed by tributaries encroach on the river valley impeding expansion of the Holocene flood plain.  

FIG. 5:  Idealized alluvium stratigraphy of San Pedro Rver.

Where the San Pedro flows across unconsolidated basin-fill sediments in the broad bottomlands near St. David, the Holocene floodplain widens dramatically, attaining widths of 1000 to 3000 ft.   

While Holocene alluvium laid down by the three rivers (in order of increasing age: Qycr, Qy4r, Qy3r, Qy2r, and Qy1r) play the chief role in conveying surface and near-surface water from adjacent surfaces – piedmont alluvium – to the river channel, some younger piedmont deposits, situated topographically above but proximal to the main trunk – notably Qyc, Qy3, and Qyaf – play a strong supporting role in water delivery from the surrounding piedmont. 

Historical Modifications and Changes in the San Pedro Valley.

As recently as the mid-19th Century, the San Pedro River was a low-energy, meandering stream with some reaches choked by extensive marshes or cienegas (Hereford, 1993).  The floodplain of the San Pedro Valley was a strip of tall range and marsh grasses dotted by sparse woody shrubs and mesquite (Hasting, 1959).  

FIG. 6: Bedrock constriction along the Babocomari River.

Beginning in the 1870’s, ranching, mining, draining cienegas – in an effort to control mosquito’s, and railroad construction – accompanied by extirpation of beaver, antelope, and many fish species – took a heavy toll on the San Pedro and its riparian environment.  By the 1930’s, the San Pedro was well into an arroyo-cutting phase and had transformed into a higher-energy stream with a deeply incised (at least locally) river channel (Cook and Reeves, 1976; Wood, 1997) (Fig. 7).  This was not the first time the San Pedro transformed from a quiet, meandering stream into a more raucous arroyo-cutting stream – episodic incision and backfilling appears to be the Holocene norm of the San Pedro River (Haynes, 1987).

The San Pedro, now alternating between a braided and meandering stream, is entrenched 5- to 20-ft along its entire length (Huckleberry, 1996).  Downcutting stranded most of the early historical floodplain, and the San Pedro’s sediment load, once a mix of sand, silts, clays and minor gravel, is now a coarse admixture of cobbles, pebbles, and sands.  Coarse-grained point bars actively form and reform on the channel floor diverting flow laterally to undercut banks and widen the channel.  Along the upper San Pedro, the channel width ranges from 120 to 240 ft; while from Redington downstream the channel swells to 300 to 600 ft wide (Huckleberry , 1996).  In the riparian zone, cottonwood, willow and sycamore have crowded out the once ubiquitous marsh grasses; north of Benson and Cascabel, invasive tamarisk fill the channel.  

Other Applications of San Pedro River Geologic Maps

FIG. 7: Incised channel of the San Pedro river.

The San Pedro geologic maps, with their focus on the areal extent and relationships of Holocene and Pleistocene Quaternary alluvium, should aid hydrologists in constraining hydrologic models along the three rivers.  For fluvial sedimentologists, the alluvial architecture inferred from the finely delineated Holocene and Pleistocene sequence provides a tool for exploring river behavior – avulsion, branching, and river response to climatic controls at glacial-interglacial cusp – over the past several million years.  Biologists investigating plant ecology may evaluate plant assemblages on different geologic units, and thus provide insight into lithologic controls on plant distribution.  And for archaeologists, the geologic maps offer a reconnaissance guide for their studies of early indigenous people of the San Pedro River valley.  With these maps in hand, land managers, policy-makers, and the communities they serve, are equipped with a powerful tool for moving towards sustainable land-use policies.

NOTE: Minor textual changes were made to this webpage post-publication (on 19 October 2009) to clarify an erroneous description of the San Pedro River as historically perennial along its length. We apologize for any confusion this may have caused.

References Cited

Amann, Jr., A.W., Bezy, J.V., Ratkevich, R. and Witkind, W.M., 1998, Ice Age Mammals of the San Pedro River Valley, Southeastern, Arizona.  Arizona Geological Survey, Down-to-Earth Series #6.

Arizona Department of Water Resources, 2009, Subflow Zone Delineation Report for the San Pedro River Watershed, .

Cook, J.P, Youberg, A., Pearthree, P.A, Onken J.A.,MacFarlane, B.J., Haddad, D.E., Bigio, E.R and Kowler, A.L, 2009,  Mapping of Holocene River Alluvium Along the San Pedro River, Aravaipa Creek, and Babocomari River, Southeastern Arizona: DM-RM-1, 6 sheets, scale 1:24,000, with text.

Cook, R.U. and Reeves, R.W., 1976, Arroyos and environmental change in the American Southwest: Oxford, Clarendon Press, 213 p.

Ferguson, T.J. and Colwell-Chanthaphonh, C, 2006, History Is in the Land

Multivocal Tribal Traditions in Arizona's San Pedro Valley, University of Arizona Press, 336 p.

Hasting 1959, Vegetation Change and Arroyo Cutting in Southeastern Arizona: Arizona Academy of Science Journal, v. 1, no. 2, p. 60-67.

Haynes, C.V., Jr., 1987, Curry Draw, Cochise County, Arizona: A Late Quaternary Stratigraphic Record of Pleistocene Extinction and Paleo-Indian Activities.  In M.L. Hill, ed, Cordilleran Section of the Geological Society of America: Geological Society of American, Centennial Field Guide Volume 1, p. 23-28.

Hereford, R., 1993, Entrenchment and widening of the upper San Pedro River, Arizona: Geological Society of America Special Paper 282, 46 p.

Huckleberry, G., 1996, Historical Channel Changes on the San Pedro River, Southeastern Arizona, by Gary Huckleberry, OFR-96-15, 35 p

Waters, M.R. and Haynes, C.V., 2001, Late Quaternary Arroyo Formation and Climate Change in the American Southwest: Geology, v. 29, no. 5, p. 399-402.

Wood, M.L., 1997, Historical channel changes along the lower San Pedro River, Southeastern Arizona: Arizona Geological Survey Open-File Report 97-21, 44 p., 3 sheets, scale 1:24,000.




AZGS Staff
Tucson, Arizona


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