Abell J, Stephens T, Hamilton DP, McBride C, Scarsbrook M. 2012. Analysis of Lake Rotorua water quality trends: 2001-2012.ERI Report No. 10. Report prepared in response to Environment Court mediation, 21 November 2012. Environmental Research Institute, University of Waikato, Hamilton. http://www.waikato.ac.nz/eri/research/publications

Abell JM, Özkundakci D, Hamilton DP, Jones JR. 2012. Latitudinal variation in nutrient stoichiometry and chlorophyll-nutrient relationships in lakes: A global study. Fundamental and Applied Limnology 181 (1): 1-14. DOI: 10.1127/1863-9135/2012/0272

Ashraf S, Brabyn L, Hick BJ. 2012. Image data fusion for the remote sensing of freshwater environments. Applied Geography 32 (2): 619 - 628. DOI: 10.1016/j.apgeog.2011.07.010

Blair JM,  Hicks BJ. 2012. Otolith microchemistry of koi carp in the Waikato region, New Zealand, a tool for identifying recruitment locations? Inland Waters 2 (3): 109-118. DOI: 10.5268/IW-2.3.480

Blair JM, Hicks BJ, Pitkethley R, Ling N. 2012. Diet of rainbow trout in Lake Rotoiti: an energetic perspective. New Zealand Journal of Marine and Freshwater Research 46 (4): 557-565. DOI: 10.1080/00288330.2012.707660

Blair JM. 2012. Factors controlling common smelt abundance and rainbow trout growth in the Rotorua Lakes, New Zealand. PhD thesis, University of Waikato, Hamilton. http://researchcommons.waikato.ac.nz/handle/10289/6941

Butterworth J. 2012. Lake Rotokakahi water quality update 1990-2011. ERI Report No. 09. Client report prepared for the Bay of Plenty Regional Council. Environmental Research Institute; University of Waikato; Hamilton. http://www.waikato.ac.nz/eri/research/publications

Carey CC, Ibelings BW, Hoffmann EP, Hamilton DP, Brookes JD. 2012. Eco-physiological adaptations that favour freshwater cyanobacteria in a changing climate.Water Research 46 (5, Special Issue): 1394-1407. DOI: 10.1016/j.watres.2011.12.016

Carraro E, Guyennon N, Hamilton D, Valsecchi L, Manfredi EC, Viviano G, Salerno F, Tartari G, Copetti D. 2012. Coupling high-resolution measurements to a three-dimensional lake model to assess the spatial and temporal dynamics of the cyanobacterium Planktothrix rubescens in a medium-sized lake.Hydrobiologia 698 (1): 77-95. DOI: 10.1007/s10750-012-1096-y.

Daniel A, Tempero G. 2012. Review of the likelihood of koi carp establishing at stormwater ponds at Totara Creek Open Space and their probable impact and options for management. Report Prepared for Thomas Civil and Environmental Consultants. University of Waikato, Hamilton.

Duggan IC, Eastwood KR. 2012. Detection and distribution of Craspedacusta sowerbii: Observations of medusa are not enough.Aquatic Invasions 7 (2): 271-275. DOI: 10.3391/ai.2012.7.2.013

Duggan IC, Robinson KV, Burns CW, Banks JC, Hogg ID. 2012. Identifying invertebrate invasions using morphological and molecular analyses: North American Daphnia 'pulex' in New Zealand fresh waters. Aquatic Invasions 7 (4): 585-590. DOI: 10.3391/ai.2012.7.4.015

Duggan IC. 2012. Urban planning provides potential for lake restoration through catchment re-vegetation.Urban Forestry and Urban Greening 11: 95-99. DOI: 10.1016/j.ufug.2011.09.006

Hamilton DP, Jones HFE, Özkundakci D, McBride C, Allan MG, Faber J, Pilditch CA. 2012. Waituna Lagoon Modelling: Developing quantitative assessments to assist with lagoon management. ERI Report No. 04. Prepared for Environment Southland. Environmental Research Institute, University of Waikato, Hamilton. http://www.waikato.ac.nz/eri/research/publications

Hamilton DP, McBride C, Özkundakci D, Schallenberg M, Verburg P, de Winton M, Kelly D, Hendy C, Ye W.2012. Effects of Climate Change on New Zealand Lakes IN: Goldman CR, Kumagai M, Robarts RD (ed.s). Climatic Change and Global Warming of Inland Waters: Impacts Mitigation for Ecosystems and Societies, John Wiley & Sons, Ltd, Chichester, UK. doi: 10.1002/9781118470596.ch19

Hicks BJ, Allen DG, Kilgour JT, Watene-Rawiri EM, Stichbury GA, Walsh C. 2012. Fishing activity in the Waikato and Waipa rivers.ERI Report No. 07. For Ministry for Primary Industries. Environmental Research Institute, University of Waikato, Hamilton.

Hicks BJ, Watene-Rawiri EM. 2012. Review of "Ikawai: freshwater fishes in Maori culture and economy". New Zealand Journal of Marine and Freshwater Research 46 (3): 437-439.DOI: 10.1080/00288330.2012.680194

Hoellein TJ, Bruesewitz DA, Hamilton DP. 2012. Are geothermal streams important sites of nutrient uptake in an agricultural and urbanising landscape (Rotorua, New Zealand)?Freshwater Biology 57 (1): 116-128. DOI: 10.1111/j.1365-2427.2011.02702.x

Kara EL, Hanson P, Hamilton DP, Hipsey MR, McMahon KD, Read JS, Winslow L, Dedrick J, Rose K, Carey CC, Bertilsson S, da Motta Marques D, Beversdorf L, Miller T, Wu C, Hsieh Y-F, Gaiser E, Kratz T. 2012. Time-scale dependence in numerical simulations: Assessment of physical, chemical, and biological predictions in a stratified lake at temporal scales of hours to months. Environmental Modelling and Software 35: 104-121. DOI: 10.1016/j.envsoft.2012.02.014

Kurian P, Wright J. 2012. Science, Governance, and Public Participation: Analysis of decision making on genetic modification in Aotearoa/New Zealand. Public Understanding of Science 21 (4). pp 378-494. DOI: 10.1177/0963662510382362

Ling N. 2012. Akerama Wetland Mitigation: Evaluation and Recommendations.CBER Contract Report No. 126. For Northern Civil Consulting Engineers Ltd. Centre for Biodiversity and Ecology Research, School of Science and Engineering, University of Waikato, Hamilton. 9 pp. http://www.waikato.ac.nz/eri/research/publications/cber-reports

Ling N. 2012. An assessment of possible impacts of water level management in the Wairua River Wildlife Management Reserve. CBER Contract Report No. 127. For Fish and Game New Zealand. Centre for Biodiversity and Ecology Research, School of Science and Engineering, University of Waikato, Hamilton. 12 pp. http://www.waikato.ac.nz/eri/research/publications/cber-reports

Mahoney BA. 2012. Determining and testing the optimal pure-tone frequency for use in acoustic conditioning of free-range carp (Cyprinus carpio). MSc thesis, University of Waikato, Hamilton. 105p. http://researchcommons.waikato.ac.nz/handle/10289/6501

Oliver R, Hamilton DP, Brookes J, Ganf GG. 2012. Physiology, blooms and prediction of planktonic cyanobacteria. Chapter 6. IN: Whitton BA (ed.). Ecology of Cyanobacteria II: Their Diversity in Space and Time, Springer, 760 pp.

Özkundakci D, Hamilton DP. 2012. Temporal coherence of water quality in mesocosms in a stratified, eutrophic lake.Journal of the Environment 8 (1): 37-46.

Özkundakci D, Hamilton DP. 2012. Review of the Waikato Regional Council shallow lakes indicators project. Waikato Regional Council shallow lakes report.

Özkundakci D, McBride CG, Hamilton DP. 2012. Parameterisation of sediment geochemistry for simulating water quality responses to long-term catchment and climate changes in polymictic, eutrophic Lake Rotorua, New Zealand. WIT Transactions on Ecology and the Environment 164: 171-182. [11th International Conference on Water Pollution: Modelling, Monitoring and Management, New Forest, UK, 10-12 July 2012. [Brebbia CA (ed), Water Pollution XI]. DOI: 10.2495/WP120151

Parkes SM, Duggan IC. 2012. Are zooplankton invasions in constructed waters facilitated by simple communities?Diversity and Distributions 18 (12): 1199-1210. DOI: 10.1111/j.1472-4642.2012.00913.x

Paul WJ, Hamilton DP, Ostrovsky I, Miller SD, Zhang A, Muraoka K. 2012. Catchment land use and trophic state impacts on phytoplankton composition: a case study from the Rotorua lakes' district. Hydrobiologia 698 (1): 133-146. DOI: 10.1007/s10750-012-1147-4

Pearson LK, Hendy CH, Hamilton DP, Silvester WB. 2012. Nitrogen-15 isotope enrichment in benthic boundary layer gases of a stratified eutrophic iron and manganese rich lake. Aquatic Geochemistry 18 (1): 1-19. DOI: 10.1007/s10498-011-9143-2

Pingram MA, Collier KJ, Hamilton DP, David BO, Hicks BJ. 2012. Carbon sources supporting large river food webs: a review of ecological theories and evidence from stable isotopes. Freshwater Reviews 5 (2): 85-103. DOI: http://dx.doi.org/10.1608/FRJ-5.2.476

Puddick J, Prinsep MR, Wood SA, Cary SC, Hamilton DP. 2012. Enhanced sample preparation for quantitation of microcystins by matrix?assisted laser desorption/ionisation-time of flight mass spectrometry. Phytochemical Analysis 23 (4): 285-291. [available online 29 Sep 2011] DOI: 10.1002/pca.1356

Purcell KM, Ling N, Stockwell CA. 2012. Evaluation of the introduction history and genetic diversity of a serially introduced fish population in New Zealand. Biological Invasions 14 (10): 2057-2065. DOI: 10.1007/s10530-012-0213-1

Read JS, Hamilton DP, Desai AR, Rose KC, MacIntyre S, Lenters JD, Smyth RL, Hanson PC, ColE JJ, Staehr PA, Rusak JA, Pierson DC, Brookes JD , Laas A, Wu CH. 2012. Lake-size dependency of wind shear and convection as controls on gas exchange. Geophysical Research Letters 39: L09405. DOI: 10.1029/2012GL051886

Rhodes L, Wood SA. 2012. Micro-algal and cyanobacterial producers of biotoxins. IN: Rossini GP (ed.). Toxins and Biologically Active Compounds from Microalgae, Science Publishers, Enfield, New Hampshire, USA.

Smith F, Wood SA, Wilks T, Kelly D, Broady P, Gaw S. 2012. Survey of Scytonema (Cyanobacteria) and associated saxitoxins in the littoral zone of recreational lakes in Canterbury (New Zealand). Phycologia 51 (5): 542-551. DOI: 10.2216/11-84.1

Tana R,  Hicks BJ. 2012. Influence of an open and closed river system on the migration patterns of two northern New Zealand populations of banded kokopu (Galaxias fasciatus). New Zealand Natural Sciences 37: 25-36. http://www.nznaturalsciences.org.nz/

Taylor CM, Duggan IC. 2012. Can biotic resistance be utilized to reduce establishment rates of non-indigenous species in constructed waters?Biological Invasions 14 (2): 307-322. DOI: 10.1007/s10530-011-0063-2

Trolle D, Hamilton, DP, Hipsey MR, Bolding K, Bruggeman J, Mooij WM, Janse JH, NielsenA, Jeppesen E, Elliott JE, Makler-Pick V, Petzoldt T, Rinke K, Flindt MR, Arhonditsis GB, Gal G, Bjerring R, Tominaga K, Hoen J, Downing AS, Marques DM, Fragoso Jr CR, Søndergaard M, Hanson PC. 2012. A community-based framework for aquatic ecosystem models. Hydrobiologia 683 (1): 25-34. DOI: 10.1007/s10750-011-0957-0

Wang S, Qian X, Han BP, Luo LC, Hamilton DP. 2012. Effects of local climate and hydrological conditions on the thermal regime of a reservoir at Tropic of Cancer, in southern China. Water Research 46 (8): 2591-2604. DOI: 10.1016/j.watres.2012.02.014

Wilding TK, Brown E, Collier KJ. 2012. Identifying dissolved oxygen variability and stress in tidal freshwater streams of northern New Zealand. Environmental Monitoring and Assessment 184 (10): 6045-6060. DOI: 10.1007/s10661-011-2402-2

Wood SA, Dietrich DR, Cary SC, Hamilton DP. 2012. Increasing Microcystis cell abundance enhances microcystin synthesis: a mesocosm study.Inland Waters 2 (1): 17-22. DOI: 10.5268/IW-2.1.424

Wood SA, Kuhajek J, de Winton M, Phillips NR. 2012. Species composition and cyanotoxin production in periphyton mats from three lakes of varying trophic status. FEMS Microbiology Ecology 79 (2): 312-326. DOI: 10.1111/j.1574-6941.2011.01217.x

Wood SA, Phillips NR, de Winton M, Gibbs M. 2012. Consumption of benthic cyanobacterial mats and nodularin-R accumulation in freshwater crayfish (Paranephrops planifrons) in Lake Tikitapu (Rotorua, New Zealand).Harmful Algae 20: 175-179. DOI: 10.1016/j.hal.2012.10.003

Wood SA, Williamson W. 2012. New Zealand: Regulation and management of cyanobacteria. IN: Chorus I (ed). Current approaches to cyanotoxin risk assessment, risk management and regulations in different countries. Federal Environmental Agency, Berlin, Germany. p 97-147.