Aldridge BMTA, Hicks BJ. 2006. The distribution of fish in the urban gully system streams of Hamilton City. CBER Contract Report No. 48. Environment Waikato and Hamilton City Council. Centre for Biodiversity and Ecology Research, School of Science and Engineering, University of Waikato, Hamilton. http://www.waikato.ac.nz/eri/research/publications/cber-reports

Ashraf S, Brabyn L, Hicks BJ. 2006. Remote sensing of freshwater habitats for large rivers and lakes of Waikato region using sub-pixel classification.CBER Contract Report No. 63. For Environment Waikato. Centre for Biodiversity and Ecology Research, School of Science and Engineering, University of Waikato, Hamilton. http://www.waikato.ac.nz/eri/research/publications/cber-reports

Bruce LC, Hamilton DP, Imberger J, Gal G, Gophen M, Zohary T, Hambright KD. 2006. A numerical simulation of the role of zooplankton in C, N and P cycling in Lake Kinneret, Israel. Ecological Modelling 193 (3-4): 412-436. DOI: 10.1016/j.ecolmodel.2005.09.008

Cary SC, Hicks BJ, Crawford NJ, Coyne K. 2006. A culture-independent approach to develop a sensitive genetic-based detection and enumeration capability for Didymosphenia geminata. CBER Contract Report No. 45. Report for MAF Biosecurity. Centre for Biodiversity and Ecology Research, School of Science and Engineering, University of Waikato, Hamilton. http://www.waikato.ac.nz/eri/research/publications/cber-reports

Chauhan M. 2006. Blue-green algae monitoring of the Rotorua Lakes. BSc (Technology) research project, University of Waikato, Hamilton.

Conn S. 2006. Use of the MCI index for evaluation of Bay of Plenty coast regions.BSc (Technology) research project, with industry partner Environment Bay of Plenty , University of Waikato, Hamilton.

Dugdale TM, Hicks BJ, De Winton M, Taumoepeau A. 2006. Fish exclosures versus intensive fishing to restore charophytes in a shallow New Zealand lake. Aquatic Conservation-Marine and Freshwater Ecosystems 16 (2):193-202 DOI: 10.1002/aqc.711

Duggan IC. 2006. The potential for inferring the trophic state of Lake Wairarapa using zooplankton community composition. CBER Contract Report No. 55. For Wellington Regional Council. Centre for Biodiversity and Ecology Research, School of Science and Engineering, University of Waikato, Hamilton. http://www.waikato.ac.nz/eri/research/publications/cber-reports

Espectacion J. 2006. Nutrient inflow into Lake Okareka via inlets. BSc (Technology) research project, University of Waikato, Hamilton.

Faithfull CL, Hamilton DP. 2006. Comparisons of densities of phytoplankton, cyanobacteria and Aulacoseira in the Waikato, 1973-2006. CBER Contract Report No. 72. For Environment Waikato. Centre for Biodiversity and Ecology Research, School of Science and Engineering, University of Waikato, Hamilton. http://www.waikato.ac.nz/eri/research/publications/cber-reports

Hamilton DP, Hamilton M, McBride CG. 2006. Nutrient and water budget for Lake Tarawera. CBER Contract Report No. 46. For Lake Tarawera Ratepayers Assn. Centre for Biodiversity and Ecology Research, School of Science and Engineering, University of Waikato, Hamilton. http://www.waikato.ac.nz/eri/research/publications/cber-reports

Hamilton DP, Hawes I, Gibbs MM. 2006. Climatic shifts and water quality response in North Island lakes, New Zealand.International Association of Theoretical and Applied Limnology Proceedings 29 (Pt 4): 1821-1824.

Hamilton DP, Kratz TK, Arzberger P, Lin F-P. 2006. Development of a Global Lake Ecological Observatory Network. Proceedings, International Workshop for Lake Observing Systems, Lake Biwa, Japan, 29-30 October 2006. p19-24.

Hicks BJ, Cary SC. 2006. Report to TAG on Genomics contract with BNZ. Report for Didymo Technical Advisory Group, MAF Biosecurity.

Hicks BJ. 2006. Goldfish: the "new" pest fish. Evidence presented in support of CBER's submission to Environment Waikato's Draft Regional Pest Management Strategy.  CBER Contract Report No. 61. A report prepared for Environment Waikato. Centre for Biodiversity and Ecology Research, Department of Biological Sciences, School of Science and Engineering, University of Waikato, Hamilton. http://www.waikato.ac.nz/eri/research/publications/cber-reports

Hopkins A. 2006. The potential for charophtye re-establishment in large, shallow, eutrophic lakes with special reference to Lake Waikare, New Zealand. MSc thesis, Biology, University of Waikato, Hamilton. http://researchcommons.waikato.ac.nz/handle/10289/2419

Jentzsch K. 2006. Genetic and morphologic examination of cyanobacteria from sediments of Lake Okaro, New Zealand. BSc thesis, Department of Chemistry, Water Sciences Programme at the University of Duisburg-Essen, Germany.

Kratz TK, Arzberger P, Benson BJ, Chiu C-Y, Chiu K, Ding L, Fountain T, Hamilton DP, Hanson PC, Hu YH, Lin F-P, McMullen R, Tilak S, Wu C. 2006. Toward a Global Lake Ecological Observatory Network. Proceedings, Karelian Institute, University of Joensuu, Finland, March 2006. 145: 51-63.

Landman MJ, van den Heuvel, MR, Finley M, Bannon HJ, Ling N.2006. Combined effects of pulp and paper effluent, dehydroabietic acid, and hypoxia on swimming performance, metabolism and hematology of rainbow trout. Ecotoxicology and Environmental Safety 65, 314-322.DOI: 10.1016/j.ecoenv.2005.10.010

Miller DC, Hicks BJ. 2006. Physical environment, nutrient budget, and ecology of Lake Moana-nui, Tokoroa.CBER Contract Report No. 42. For South Waikato District Council & Environment Waikato. Centre for Biodiversity and Ecology Research, School of Science and Engineering, University of Waikato, Hamilton. http://www.waikato.ac.nz/eri/research/publications/cber-reports

Özkundacki D. 2006. Efficacy of sediment capping materials and flocculants for nutrient removal as a lake restoration technique. BSc Dip thesis, University of Applied Sciences, Germany.

Özkundakci D, Hamilton DP. 2006. Recent studies of sediment capping and flocculation for nutrient stabilisation. CBER Contract Report No. 53. Report prepared as part of the Lake Ecosystem Restoration New Zealand (LERNZ). Centre for Biodiversity and Ecology Research, School of Science and Engineering, University of Waikato, Hamilton. http://www.waikato.ac.nz/eri/research/publications/cber-reports

Ryan EF, Duggan IC, Hamilton DP, Burger DF. 2006. Phytoplankton assemblages in North Island lakes of New Zealand: is trophic state, mixing, or light climate more important? New Zealand Journal of Marine and Freshwater Research 40 (3): 389-398. DOI: 10.1080/00288330.2006.9517430

Sutherland DL. 2006. Phylogeography and ecology of New Zealand freshwater Amphipoda (Paracalliope, Paraleptamphopus and Phreatogammarus). PhD thesis, University of Waikato, Hamilton. 183pp. http://researchcommons.waikato.ac.nz/handle/10289/2650

Taylor S, Landman MJ, Ling N. 2006. Flow cytometric characterization of freshwater crayfish (Paranephrops planifrons) hemocytes for the examination of physiological status in wild and captive animals.Journal of Aquatic Animal Health 21: 195-203. DOI: 10.1577/H09-003.1

Tempero GW, Ling N, Hicks BJ. 2006. Age composition, growth, and reproduction of koi carp (Cyprinus carpio) in the lower Waikato region, New Zealand. New Zealand Journal of Marine and Freshwater Research 40: 571-583. DOI: 0028-8330/06/4004-0571

West DW, Ling N, Hicks BJ, Tremblay LA, Kim, ND, van den Heuvel MR. 2006. Cumulative impacts assessment along a large river, using brown bullhead catfish (Ameiurus nebulosus) populations. Environmental Toxicology and Chemistry 25 (7): 1868-1880. DOI: 10.1897/05-315R.1