Fossil Creek Software

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Selected publications

Available modeling and other publications include:

Milhous, Robert T. and John M. Bartholow.  2010.  Environmental Flow Issues in the Poudre River, Colorado, USA.  In Proceedings, ISE 2010, 8th International Symposium on Ecohydraulics 2010.  September 12-16, 2010 COEX, Seoul, Korea.  Korea Water Resources Association (KWRA).  pp 1469-1476.  (CD- paper S7B-1).  Available online here.

Bartholow, J.M.  2010.  Constructing an interdisciplinary flow regime recommendation.  J. Am. Water Resources Association 1-15.  DOI: 10.1111/j.1752-1688.2010.00461.x.  Available online here .  Preprint using English units available here.

Campbell, S., Bartholow, J., and Heasley, J., 2010, Application of the Systems Impact Assessment Model (SIAM) to fishery resource issues in the Klamath River, California: U.S. Geological Survey Open-File Report 2009- 1265, 74 p.

McCullough, Dale A., Bartholow, John M., Jager, Henriëtte I., Beschta, Robert L., Cheslak, Edward F., Deas, Michael L., Ebersole, Joseph L., Foott, J. Scott, Johnson, Sherri L., Marine, Keith R., Mesa, Matthew G., Petersen, James H., Souchon, Yves, Tiffan, Kenneth F. and Wurtsbaugh, Wayne A. 2009.  Research in Thermal Biology: Burning Questions for Coldwater Stream Fishes.  Reviews in Fisheries Science 17(1):90–115.

Bovee, K.D., T.J. Waddle, J. Bartholow, and L. Burris. 2007. A decision support framework for water management in the upper Delaware River. USGS Open-File Report 2007-1172. : U.S. Geological Survey. 122 p.

Bartholow, J.  2007.  Economic Benefit of Fertility Control in Wild Horse Populations.  Journal of Wildlife Management 71(8):2811–2819.

Bartholow, J.M. and J. Heasley. 2006. Evaluation of Shasta Dam scenarios using a salmon Production Model. USGS Administrative Report, August 17, 2006, Fort Collins, Colo. 110 p.

Milhous, R.T. and J.M. Bartholow. 2006. Two analytical approaches for quantifying physical habitat as a limit to aquatic ecosystems. Journal of River Basin Management 4(3). Available on the Internet at

Bartholow, J.M. and J.A. Henriksen. 2006. Assessment of Factors Limiting Klamath River Fall Chinook Salmon Production Potential Using Historical Flows and Temperatures. USGS Open File Report 2006–1249. 111 p. Available on the Internet at

Bartholow, J.M. and J. Heasley. April 28, 2005. Upper Delaware River Temperature Modeling: Phase I Final Report. 50 pp.

Bartholow, J.M., and J. Heasley. 2005. JC Boyle Bypass Segment Temperature Analysis. USGS Administrative Report. Fort Collins Science Center, Fort Collins, Colorado. 24 pp.

Bartholow, J.M. 2005. Recent Water Temperature Trends in the Lower Klamath River, California. North American Journal of Fisheries Management 25(1): 152–162.

Bartholow, J.M. 2005. Modeling Chinook salmon with SALMOD on the Sacramento River, California. Hydroecol. Appl. 14(1):193-219.

Bartholow, J.M., J. Heasley, R.B. Hanna, J. Sandelin, M. Flug, S. Campbell, J. Henriksen, and A. Douglas. 2005. Evaluating Water Management Strategies with the Systems Impact Assessment Model: SIAM Version 4. Revised March 2005. U.S. Geological Survey, Fort Collins Science Center Open File Report 03-82. Fort Collins, Colorado. March 2003. 133 pp. Available on the Internet at

Bartholow, J.M., S. Campbell, and M. Flug. 2004. Predicting the thermal effects of dam removal on the Klamath River. Environmental Management, 34(6):856-874.

Bartholow, J.M. 2004. An economic analysis of alternative fertility control and associated management techniques for three BLM wild horse herds. USGS Open File Report 2004-1199. 33 pp. Available on the Internet at

Sedgwick, J. and J. Bartholow. 2004. Fox on a hot tin roof. Western North American Naturalist 64(3):406-408.

Bartholow, John M. 2003. Modeling Chinook Salmon with SALMOD on the Sacramento River. Chapter 14 in B.L. Lamb, D. Garcia de Jalon, C. Sabaton, Y. Souchon, N. Tamai, H.R. Robinette, T.J. Waddle, and A. Brinson, Editors. Proceedings of the International IFIM Users' Workshop. Fort Collins, Colorado, USA: Colorado State University, Office of Conference Services. paper at

Bartholow, J.M., J. Heasley, R.B. Hanna, J. Sandelin, M. Flug, S. Campbell, J. Henriksen, and A. Douglas. 2003. Evaluating Water Management Strategies with the Systems Impact Assessment Model: SIAM Version 3. U.S. Geological Survey, Fort Collins Science Center Open File Report 03-82. Fort Collins, Colorado. March 2003. 128 pp. Available on the Internet at

Bartholow, J.M. 2003. Modeling Uncertainty: Quicksand for Water Temperature Modeling. Pages 221 to 232 in Hydrological Science and Technology 19(1-4), Proceedings of American Institute of Hydrology conference on Hydrologic Extremes: Challenges for Science and Management. October 13-17, 2002, Portland, OR. Also available on the Internet at

Bartholow, J.M. 2002. SNTEMP (In)Frequently Asked Questions. Available on the Internet at

Bartholow, J., 2002, Stream Segment Temperature Model (SSTEMP) Version 2.0: Fort Collins, CO, U.S. Geological Survey, 29 p. Computer program and user documentation available at

Bartholow, J. and B. Milhous. 2002. What Records Have We Been Breaking? Colorado Climate 3(3):1-4.

Saito, L. B.M. Johnson, J. Bartholow, R. B. Hanna. 2001. Assessing Ecosystem Effects of Reservoir Operations Using Food Web-Energy Transfer and Water Quality Models. Ecosystems 4(2):105-125.

Bartholow, J., Heasley, J., Sandelin, J., Coughlan, B.A.K., Laake, J., and Moos, A. 2001. Salmod: a population model for Salmonids: User's Manual. Version 2.0. USGS/FORT Internal Publication. 89 pp. Available on the Internet at

Bartholow, J.M. 2001. Book Review: A review and synthesis of effects of alterations to the water temperature regime on freshwater life stages of salmonids, with special reference to chinook salmon. By D.A. McCullough. Transactions of the American Fisheries Society 130(2):350.

Bartholow, J.M., R.B. Hanna, L. Saito, D. Lieberman, and M. Horn. 2001. Simulated limnological effects of the Shasta Lake temperature control device. Environmental Management 27(4):609-627. Available for some domains on the Internet at or at

Bartholow, J.M., 2000, Estimating cumulative effects of clearcutting on stream temperatures, Rivers, 7(4), 284-297. Also available on the Internet at

Bartholow, J.M. 2000. The Stream Segment and Stream Network Temperature Models: A Self-Study Course, Version 2.0. U.S. Geological Survey Open File Report 99-112. 276 pp. Available on the Internet at

Hanna, R.B., L. Saito, J.M. Bartholow, and J. Sandelin. 1999. Results of simulated temperature control device operations on in-reservoir and discharge water temperatures using CE-QUAL-W2. J. of Lake and Reservoir Management 15(2):87-102. Portions available over the Internet at

Bovee, K.D., B.L. Lamb, J.M. Bartholow, C.B. Stalnaker, J. Taylor and J. Henriksen. 1998, Stream habitat analysis using the instream flow incremental methodology. U.S. Geological Survey, Biological Resources Division Information and Technology Report USGS/BRD-1998-0004. Viii +131 pp.

Bartholow, J., and J. Sandelin. 1998. Getting results with SIAM for the Klamath River. USGS/BRD/MESC internal publication. 55 pages. [Also available along with the software on the Internet.]

Bartholow, J. 1998. Animation of "Age of Water" in Shasta Lake for 1995. Web based product.

Bartholow, J., J. Sandelin, B.A.K. Coughlan, J. Laake, and A. Moos. October 1997. SALMOD: A Population Model for Salmonids: User's Manual. Version 2.0. USGS/MESC Internal Publication. 89 pp. [Also available over the Internet]

Saito, L., and J. Bartholow. 1997. Summary of Water Temperature Calibration for a CE-QUAL-W2 Model of Shasta Lake, California. [Reproduction of workshop proceedings.]

Bartholow, J.M. 1996. Sensitivity of a salmon population model to alternative formulations and initial conditions. Ecological Modeling 88(1-3):215-226.

Bartholow, J., A.J. Douglas, and J.G. Taylor. 1995. Balancing hydropower and environmental values: The resource management implications of the US Electric Consumers Protection Act and the AWARETM software. Environmental Values 4(3):257-270.

Stalnaker, C., B.L. Lamb, J. Henriksen, K. Bovee, and J. Bartholow. 1995. The Instream Flow Incremental Methodology. A primer for IFIM. U.S. National Biological Service Biological Science Report 29. 44 pp.

Bartholow, J.M., J.L. Laake, C.B. Stalnaker, and S.C. Williamson. 1993. A salmonid population model with emphasis on habitat limitations. Rivers 4(4):265-279. (Contact me for PDF.)

Williamson, S.C., J.M. Bartholow, and C.B. Stalnaker. 1993. Conceptual model for quantifying pre-smolt production from flow-dependent physical habitat and water temperature. Regulated Rivers: Research & Management. 8(1&2):15-28.

Bartholow, J.M. 1991. A modeling assessment of the thermal regime for an urban sport fishery. Environmental Management. 15(6):833-845.  Available here.

Bartholow, J. and W. Slauson. 1990. (Comments) Questions on Habitat Preference. North American Journal of Fisheries Management. 10:362-363.

Milhous, R.T., J.M. Bartholow, M.A. Updike, and A.R. Moos. 1990. Reference Manual for Generation and Analysis of Habitat Time Series -- Version II. US Fish Wildl. Serv., Biol. Rep. 90(16). 249 pp.

Bartholow, J.M. 1989. Stream temperature investigations: field and analytic methods. Instream Flow Information Paper No. 13. U.S. Fish Wildl. Serv. Biol. Rep. 89(17). 139 pp.

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