- Bailey Barrett, K., J.M. Haynes, and D.I. Warton. 2017. Thirty years of change in a benthic macroinvertebrate community of southwestern Lake Ontario after invasion by four Ponto-Caspian species. Freshwater Science 36(1): 90-102.
- DiSalvo*, B.C., and J.M. Haynes. 2015. Colonization and persistence of Crangonyx pseudogracilis (Bousfield 1958) in temporary pools. Freshwater Science 34(2): 547-554.
- Pelletier, M., J.M. Haynes, A.M Dungan*, and J. Kroeckel*. 2014. Characterization of the microbial population around San Salvador Island, Bahamas. The International Journal of Bahamian Studies 20(1): 27-37
- Wells, S.M.*, and J.M. Haynes. 2013. Fish-habitat relationships in the Tonawanda and Johnson Creek Watersheds of Western New York State, USA. Journal of Ecology and the Natural Environment 5: 396-406.
- Chalupnicki, M.A.*, and J.M. Haynes. 2011. Health of Brockport Creek following removal of contaminated sediment from an upstream tributary. Journal of Environmental Chemistry and Ecotoxicology 5(3): 127-128.
- Wellman,S.T.*, and J.M. Haynes. 2010. Diel activity patterns of Mink, Neovison vison, change with habitat. Canadian Field-Naturalist 4(124): 368-370.
Haynes, and S.T. Wellman*. 2009. Total PCBs, dioxin-furan TEQs and total mercury concentrations in mink in and out of the Rochester Embayment Area of Concernshore of Lake Ontario. Archiv. Environ. Contam.Toxicol. 57(4): 794-802.
Haynes, J. M., S.T. Wellman*, K.J. Beckett, J.J. Pagano, S.D. Fitzgerald, and S.J. Bursian. 2009. Histological lesions in mink jaws are a highly sensitive biomarker of effect after exposure to TCDD-like chemicals: field and literature-based confirmations. Archiv. Environ. Contam.Toxicol. 57(4): 803-807.
- Wellman*, S.T., J.M. Haynes, and J.J. Pagano. 2009. Model estimates bioaccumulation of total PCBs, dioxin-furan TEQs, and total mercury in mink liver based on concentrations in Lake Ontario water. Archiv. Environ. Contam.Toxicol. 57(4): 808-815
- Foust*, J.C., and J.M. Haynes. 2007. Failure of walleye recruitment in a lake with little suitable spawning habitat is probably exacerbated by restricted home ranges. J. Freshwater Ecol. 22(2): 297-309.
- Walter*, R.P., and J.M. Haynes. 2006. Fish and coral community structure are related on shallow water patch reefs near San Salvador, Bahamas. Bull. Marine Sci. 79(2): 365-374.
- Halbrend*, S.W., S.D. Hile*, J.M. Haynes, and B.R. Roosa. 2006. Rock bass learn to associate food with a visual cue and remember the association when food is absent. J. Freshwater Ecol. 21(3): 391-397.
- Hughes*, T.C., C.E. Lowie and J.M. Haynes. 2005. Age, growth, relative abundance, and scuba capture of a new or recovering population of lake sturgeon in the lower Niagara River, New York. N. Am. J. Fish. Mgmt. 25: 1263-1272.
Haynes, J.M., N.A. Tisch, C.M. Mayer and R.S. Rhyne*. 2005. Benthic macroinvertebrate communities in southwestern Lake Ontario following invasion of Dreissena and Echinogammarus: 1983 – 2000. J. N. American Benthological Society. 24(1): 148-167.
Haynes, J.M., M.M. Hluchy, and M.R. Connolly. 2004. Disseminating successful undergraduate science curriculum adaptation and implementation strategies and CCLI grant-writing Techniques: Regional workshops led by successful innovators and experienced investigators, evaluating faculty change processes, and assessing student understanding of STEM concepts. Pages 227-331, in Invention and Impact: Building Excellence in Undergraduate Science, Technology, Engineering and Mathematics (STEM) Education. American Association for the Advancement of Science. Washington, DC.
- Lowie*, C.E., and J.M. Haynes. 2001. Comparison of walleye habitat suitability index (HSI) information with habitat features of a walleye spawning stream. J. Freshwater Ecol.: 621-631.
Haynes, J.M., T.W. Stewart and G.E. Cook*. 1999. Benthic macroinvertebrate communities in southwestern Lake Ontario following invasion of Dreissena: continuing change. J. Great Lakes Res. 25(4):828-838.
Haynes, J.M. 1998. Stressed stream analysis: addressing real environmental problems in local communities to stimulate undergraduate science faculty and students. J. Coll. Sci. Teach. 28(1):43-51.
Haynes, J.M. 1997. Zebra mussels and benthic macroinvertebrate communities of southwestern Lake Ontario and selected tributaries: unexpected results? Great Lakes Res. Rev. 3(1):9-16.
- Miller*, S.J., and J.M. Haynes. 1997. Factors limiting colonization in western New York creeks by the zebra mussel, Dreissena polymorpha. J. Freshwater Ecol. 12(1):81-88.
- Haynes, J.M. 1995. Thermal ecology of salmonids in Lake Ontario. Great Lakes Res. Rev.> 2(1):17-22.
Stewart*, T.W., and J.M. Haynes. 1994. Benthic macroinvertebrate community changes following zebra mussel (Dreissena polymorpha) invasion of southwestern Lake Ontario. J. Great Lakes Res. 20(2):479-493.
- Aultman*, D.C., and J.M. Haynes. 1993. Spring thermal fronts and salmonine sport catches in Lake Ontario. N. Amer. J. Fish. Mgmt. 13(3):502-510.
- Haynes, J.M., G.P. Gerber* and J.K. Buttner. 1989. Response of sport fishes to thermal discharges in the Great Lakes: is Somerset Station, Lake Ontario, different? J. Great Lakes Res. 15(4):709-718.
- Haynes, J.M., and G.P. Gerber*. 1989. Movements and temperatures of radiotagged salmonines in Lake Ontario and comparisons with other large aquatic systems. J. Freshwater Ecol. 5(2):197-204.
*denotes student author
- Haynes, J.M., K.F. Korfmacher, and E.J. Mellas. 2010-2012. GLISTEN collaborative cluster planning and implementation. Great Lakes Innovative Stewardship Through Education Network, National Center for Science and Cooperative Education.
- Haynes, J.M., and G. Neuderfer. 2010-2011. Water quality monitoring for the Remedial Action Plan. Monroe County Dept. of Health.
- Haynes, J.M., and J.A. Zollweg. 2005-2006. Distribution of host fishes for listed and rare freshwater mussel species, and of state-listed fishes, in Muddy Creek on the Erie National Wildlife Refuge. US Fish and Wildlife Service.
- Haynes, J.M. 2004-2006. Status of longear sunfish populations in western New York. NY Dept. of Environmental Conservation.
- Haynes, J.M. 2004. Benthic macroinvertebrates of the Irondequoit Bay wetland. Monroe County Dept. of Health.
- Haynes, J.M., J.J. Pagano and S.T. Wellman. 2003-2006. RAP progress in the Rochester Embayment of Lake Ontario: Population monitoring and levels of bioaccumulative chemicals of concern in mink, a sentinel species. New York Great Lakes Protection Fund.
- Haynes, J.M. 2002. Biological study of Irondequoit Bay. Monroe County Department of Planning and Development.
- Haynes, J.M. 2002-2010. Fishery study of Waneta and Lamoka Lakes. Waneta-Lamoka Lakes Association.
- Haynes, J.M., S.M. Millar and M.M. Hluchy. 2001-2006. Assessment and evaluation supplement to “Regional Workshops Led by Successful Innovators and Experienced Investigators.” National Science Foundation.
- Haynes, J.M. and M.M. Hluchy. 2000-2005. Disseminating successful undergraduate science curriculum development, adaptation and implementation strategies and CCLI grant writing techniques: regional workshops led by successful innovators and experienced investigators. National Science Foundation.
- Haynes, J.M. and J.C. Makarewicz. 2000-2002. Measuring RAP progress in the Rochester Embayment of Lake Ontario: determining baseline levels of bioaccumulative chemicals of concern in air, water, sediment and sentinel species. NY Great Lakes Protection Fund.
- Haynes, J.M., J. Chiarenzelli, A. Nelson, J. Pagano and T.C. Young. 1999-2001. Academic program assessment. Great Lakes Research Consortium.
- Tisch, N., J.M. Haynes and C. Mayer. 1999. Impact assessment of the introduced amphipod, Echinogammarus ischnus, in the Great Lakes. Great Lakes Research Consortium.
- Makarewicz, J.C. and J.M. Haynes (Principal Investigators) and R.C. Dilcher, J.C. Hunter and C.J. Norment (Co-Principal Investigators). 1999. Biological survey of Yanty Creek Marsh. NY Office of Parks, Recreation and Historic Preservation.
- Haynes, J.M. (Lead Instructor), and seven co-investigators. 1998-99, 1996-97, 1994-95, 1993-93, 1990-91. Great Lakes Research Consortium summer practicum for applied environmental problem-solving: new approaches and techniques for undergraduate faculty. National Science Foundation, Undergraduate Faculty Enhancement Program.
- Haynes, J.M. (Project Director), and six co-investigators. 1997-98, 1995-96, 1993-94. Stressed Stream Analysis: addressing real environmental problems to stimulate undergraduate faculty. National Science Foundation, Undergraduate Faculty Enhancement Program.
- Haynes, J.M. 1996-97. Macroinvertebrate survey, sampling strategy, and biotic index for the Irondequoit Creek wetland. Monroe County Dept. of Health.
- Haynes, J.M. 1994-95. Community ecology of the Niagara County artificial reef and nearby natural areas of Lake Ontario. U.S. Fish and Wildlife Service.
- Haynes, J.M. 1994. Survey of Buttonwood Creek, Monroe County, NY to determine habitat availability for and relative abundance of a species of special concern, the pirate perch(Aphredoderus sayanus). Monroe County Dept. of Transportation.
- Haynes, J.M. 1992-93. Deployment and recovery of sediment samplers and side-scan sonar in Lake Ontario. SUNY at Stony Brook.
- Haynes, J.M. 1991. Relative fish abundance at an artificial reef in Lake Ontario. Niagara County Department of Planning and Industrial Development.
- Haynes, J.M. 1990. Sediment sampling and analysis, Braddock Bay, Lake Ontario. Town of Greece, NY.
- Haynes, J.M., and N.J. Frisch. 1989-90. Illustrated guide and slide set for Hudson River fishes. Hudson River Foundation.
*denotes student contributor