Arbuckle, C.J., Bell, R., McCutchen, D., Ranum, A., Rufaut, C., 1993:  The use of aerial surveys to quantify the distribution of fur seals (Arctocephalus forsteri) on the Otago Peninsula. University of Otago Wildlife Management. Report Number 34.

Arbuckle, C.J.A.H., 1995:  Applications of Remote Sensing and Geographic Information Systems to Wetland Inventory: Problems of data acquisition, accuracy and application. University of Otago Wildlife Management. Report Number 69.

Townsend, C. R., Arbuckle, C. J., T. A. Crowl, and M. R. Scarsbrook. 1997. The relationship between land use and physicochemistry, food resources and macroinvertebrate communities in tributaries of the Taieri River, New Zealand: a hierarchically scaled approach. Freshwater Biology 37: 177-191.

Arbuckle, C.J., Huryn, A.D., Israel, S,.1998Applications of Remote Sensing and GIS to Wetland Inventory: upland bogs. C.J Arbuckle, Proceedings of the SIRC’98: Tenth Annual Colloquium of the Spatial Information Research Centre: University of Otago, Dunedin, New Zealand.

Arbuckle, C.J., Huryn, A.D., Israel, S. 1999. Land cover classification in the Taieri River Catchment, New Zealand:  A focus on the Riparian Zone Geocarto International 14 (3) 7-13.

Matthaei, C.D, Arbuckle, C.J. Townsend, C.R. 2000. Stable surface stones as refugia for invertebrates during disturbance in a New Zealand stream. Journal of the North American Benthological Society 19 (1) 82-93.

Whitmore, N., Huryn, A.D., Arbuckle, C.J. Jansma, F. 2000. Ecology and distribution of the freshwater crayfish Paranephrops zealandicus in Otago: implications for conservation. Department of Conservation. Science for Conservation Report 148, 42pp.

Biggs, B. J. F., Francoeur, S., Huryn, A.D., Young, R., Arbuckle, C.J., Townsend, C.R. 2000 Trophic cascades in streams: effects of nutrient enrichment on autotrophic and consumer benthic communities under two different fish predation regimes. Canadian Journal of Fisheries and Aquatic Sciences 57 (7) 1380-1394.

Huryn, A.D., Riley, R., Young, R., Arbuckle, C.J., Peacock, K., Lyon. 2000 Temporal shift in contribution of terrestrial organic matter to consumer production in a grassland riverFreshwater Biology 46 (2) 213-226.

Broad, T.L, C.R Townsend, C J Arbuckle and D.J Jellyman. 2000 A model to predict the presence of longfin eels in some New Zealand streams, with particular reference to riparian vegetation and elevation. Journal of Fish Biology 58, 1098-1112.

Huryn, A.D., V.M. Butz Huryn, L. Tsomides and C.J. Arbuckle 2000.Catchment land-use, macroinvertebrates and detritus processing in headwater streams: taxonomic richness versus function. Freshwater Biology. 47 401-415

Huryn, A.D., R. Riley, R.G. Young, K. Peacock, C.J. Arbuckle and G. Lyon. 2001. Temporal shift in contribution of terrestrial organic matter to consumer production in a grassland river. Freshwater Biology 46:213-226.

Huryn, A.D., R. Riley, R.G. Young, K. Peacock and Arbuckle C.J,. (2002). Natural abundance stable C and N isotopes indicate weak upstream-downstream linkage of food webs in a grassland river. Archiv für Hydrobiologie 153: 177-196.

David, B, Closs, G. and C.J. Arbuckle. (2002) Distribution of fish in the tributaries of the lower Taieri/Waipori Rivers, South Island, New Zealand. New ZealandJournal of Marine and Freshwater Research 36 797-808.

Townsend, C.R., Dolédec, S, Norris, R., Peacock, K and Arbuckle, C.J. (2003)The influence of scale and geography on relationships between stream community composition and landscape variables: description and prediction. Freshwater Biology 48: 768-785.

Brosse, S., Arbuckle, C. and Townsend, C.R. (2003)Habitat scale and biodiversity: influence of catchment, stream reach and bedform scales on local insect diversity. Biodiversity and Conservation 12: 2057-2075.

Riley, R.H., Townsend C.R., Niyogi, D.K., Arbuckle, C.J. and Peacock, K. (2003)Headwater stream response to grassland agricultural development in New Zealand. New ZealandJournal for Marine and Freshwater Research 37: 389-403.

Townsend, C.R., Downes, B.J., Peacock, K. & Arbuckle, C.J. (2004)Scale and the detection of land-use effects on morphology, vegetation and macro-invertebrate communities of grassland streams. Freshwater Biology49: 448-462.

Leprieur, F., Hickey M.A., Arbuckle C.J., Closs, G.P., Brosse, S., and C.R. Townsend, (2006).Hydrological disturbance benefits a native fish at the expense of an exotic fish in a New Zealand River catchment. Applied Ecology 43: 930-939.

Hilton, M. J., Harvey, Nicholas, Hart, A., James, K. F., Arbuckle, C. (2006) The impact of exotic dune grass species on foredune development in Australia and New Zealand: a case study of Ammophila arenaria and Thinopyrum junceiforme , Australian Geographer, 37 (3):313-334.

Niyogi, D K. Koren, M, C J Arbuckle, and Townsend, C.R (2007) Stream Communities along a land-use gradient: subsidy stress responses to pastoral development, Environmental Management 39: 213-225.

Niyogi, D K. Koren, M, C J Arbuckle, and Townsend, C.R (2007) Longitudinal changes in biota along four New Zealand streams: declines and improvements in stream health related to land use. New Zealand Journal of Marine and Freshwater Research 41: 63-75.

Schallenburg, M, Larned, S, Hayward S, Arbuckle C (2010) Effect of opening regime on water quality in two intermittently closed and open lagoons, South Island New Zealand. Estuarine and Coastal Shelf Management Vol 86 (4): 587-597

Book Chapters

Matthaei, C.D., Townsend, C.R., Arbuckle, C.J., Peacock, K.A., Guggelberger, C., Küster, C.E. & Huber, H. 2004. Disturbance, assembly rules and benthic communities in running waters: a review and some implications for restoration projects.  Pages 367-388 in Assembly Rules and Restoration Ecology Bridging the Gap between Theory and Practice (editors Temperton, V., Hobbs, R., Nuttle, T. & Halle, S.). Island Press, Washington.