* Includes a bibliography of papers that cite the MCI (and variants), not all of which are cited in this report.
Armitage PD, Moss D, Wright JF, Furse MT. 1983. The performance of a new biological water quality score system based on macroinvertebrates over a wide range of unpolluted running water sites. Water Research 17: 333-47.
Artemiadou V, Lazaridou M. 2005. Evaluation score and interpretation index for the ecological quality of running waters in central and northern Hellas. Environmental Monitoring and Assessment 110(1-3): 1-40.
Benjamini Y, Hochberg Y. 1995. Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society B (57): 289-300.
Biggs BJF, Close ME. 1989. Periphyton biomass dynamics in gravel bed rivers: the relative effects of flows and nutrients. Freshwater Biology 22: 209-31.
BMWP. 1978. Final report: assessment and presentation of the biological quality of rivers in Great Britain. Unpublished report, Biological Monitoring Working Party. London: Department of the Environment, 37 p.
*Boothroyd IKG, Stark JD. 2000. Use of invertebrates in monitoring. In: Collier KJ, Winterbourn MJ (eds) New Zealand Stream Invertebrates: Ecology and implications for management, pp. 344-73. Christchurch: New Zealand Limnological Society.
Borja A, Muxika H. 2005. Guidelines for the use of AMBI (AZTI's Marine Biotic Index) in the assessment of the benthic ecological quality. Marine Pollution Bulletin 50(7): 787-9.
Chessman BC. 1995. Rapid assessment of rivers using macroinvertebrates: a procedure based on habitat-specific sampling, family-level identification and a biotic index. Australian Journal of Ecology 20: 122-9.
Chessman BC. 2003. New sensitivity grades for Australian river macroinvertebrates. Marine and Freshwater Research 54: 95-103.
Chessman BC, Growns JE, Kotlash AR. 1997. Objective derivation of macroinvertebrate family sensitivity grade numbers for the SIGNAL biotic index: application to the Hunter River system, New South Wales. Marine and Freshwater Research 48: 159-72.
Chessman BC, Trayler KM, Davis JA. 2002. Family- and species-level biotic indices for macroinvertebrates of wetlands on the Swan Coastal Plain, Western Australia. Marine and Freshwater Research 53: 919-30.
Chutter FM. 1972. An empirical biotic index of the water quality in South African streams and rivers. Water Research 6: 19-30.
Clarke RT, Wright JF, Furse MT. 2003. RIVPACS models for predicting the expected macroinvertebrate fauna and assessing the ecological quality of rivers. Ecological Modeling 160(3): 219-33.
*Collier KJ. 1995. Environmental factors affecting the taxonomic composition of aquatic macroinvertebrate communities in lowland waterways of Northland, New Zealand. New Zealand Journal of Marine and Freshwater Research 29: 453-65.
*Collier KJ, Kelly J. 2006. Patterns and trends in the ecological condition of Waikato streams based on the monitoring of aquatic invertebrates from 1994 to 2005. Environment Waikato Technical Report 2006/04, 28 p.
*Collier KJ, Wilcock RJ, Meredith AS. 1998. Influence of substrate type and physico-chemical conditions on macroinvertebrate faunas and biotic indices of some lowland Waikato, New Zealand, streams. New Zealand Journal of Marine and Freshwater Research 32: 1-19.
Coysh J, Norris R. 1999. Waikato Region AusRivAS Trial Draft Report. SMF Contract No. 5091 prepared for the Ministry for the Environment.
Davies PE. 1997. Development of a national river bioassessment system (AUSRIVAS) in Australia. In: Wright JW, Sutcliffe DW, Furse MT (eds) Assessing the Biological Quality of Fresh Waters, RIVPACS and Other Techniques, pp. 113-24. Ambleside, Cumbria: Freshwater Biological Association.
Davy-Bowker J, Murphy JF, Rutt GR, Steel JEC, Furse MT. 2005. The development and testing of a macroinvertebrate biotic index for detecting the impact of acidity on streams. Archiv fur Hydrobiologie 163(3): 383-403.
*Death RG, Baillie B, Fransen P. 2003. Effect of Pinus radiata logging on stream invertebrate communities in Hawke's Bay, New Zealand. New Zealand Journal of Marine and Freshwater Research 37: 507-20.
De Pauw N, Roels D, Fontoura AP. 1986. Use of artificial substrates for standardized sampling of macroinvertebrates in the assessment of water quality by the Belgian Biotic Index. Hydrobiologia 133: 237-58.
*Doledec S, Phillips N, Scarsbrook M, Riley RH, Townsend CR. 2006. Comparison of structural and functional approaches to determining land-use effects on grassland stream invertebrate communities. Journal of the North American Benthological Society 25(1): 44-60.
*Duggan IC, Collier KJ, Lambert PW. 2002. Evaluation of invertebrate biometrics and the influence of subsample size using data from some Westland, New Zealand, lowland streams. New Zealand Journal of Marine and Freshwater Research 36: 117-28.
*Duggan IC, Scarsbrook MR, Quinn JM. 2003. Comparison of coded abundance and fixed count rapid assessment techniques for biomonitoring New Zealand streams. New Zealand Journal of Marine and Freshwater Research 37: 23-9.
Elliott JM. 1977. Some methods for the statistical analysis of samples of benthic invertebrates (2nd ed). Scientific Publications of the Freshwater Biological Association 25, 156 p.
Graca MAS, Coimbra CN. 1998. The elaboration of indices to assess biological water quality: a case study. Water Research 32: 380-92.
*Hall MJ, Closs GP, Riley RH. 2001. Relationships between land use and stream invertebrate community structure in a South Island, New Zealand, coastal stream catchment. New Zealand Journal of Marine and Freshwater Research 35(3): 591-604.
Herlihy AT, Larsen DP, Paulsen SG, Urquhart NS, Rosenbaum BJ. 2000. Designing a spatially balanced, randomized site selection process for regional stream surveys: the EMAP Mid-Atlantic Pilot Study. Environmental Monitoring and Assessment 63(1): 95-113.
Herricks EE, Cairns J. 1982. Biological monitoring Part III: receiving system methodology based on community structure. Water Research 16: 141-53.
*Hickey CW, Clements WH. 1998. Effects of heavy metals on benthic macroinvertebrate communities in New Zealand streams. Environmental Toxicology and Chemistry 17(11): 2338-46.
Hickey CW, Quinn JM, Davies-Colley RJ. 1989. Effluent characteristics of dairy shed oxidation ponds and their potential impacts on rivers. New Zealand Journal of Marine and Freshwater Research 23: 569-84.
Hilsenhoff WL 1977. Use of arthropods to evaluate water quality of streams. Technical Bulletin 100. Madison, Wisconsin, USA: Department of Natural Resources, 15 p.
Hilsenhoff WL. 1987. An improved biotic index of organic stream pollution. Great Lakes Entomologist 20: 31-9.
Hilsenhoff WL. 1988. Rapid field assessment of organic pollution with a family-level biotic index. Journal of the North American Benthological Society 7: 65-8.
Hirsch A. 1958. Biological evaluation of organic pollution of New Zealand streams. New Zealand Journal of Science 1: 500-51.
Jiang HG. 2006. Development of a new biotic index to assess freshwater pollution. Environmental Pollution 139(2): 306-17.
*Joy MK, Death RG. 2003. Biological assessment of rivers in the Manawatu-Wanganui region of New Zealand using a predictive macroinvertebrate model. New Zealand Journal of Marine and Freshwater Research 37: 367-79.
Karr JR, Chu EW. 1999. Restoring Life in Running Waters: Better biological monitoring. Washington DC: Island Press, 206 p.
Katoh K. 1992. A comparative study of some ecological methods of evaluation of water pollution. Environmental Science 5: 91-8.
Lawrence TM, Harris TL. 1979. A quantitative method for ranking the water quality tolerances of benthic species. Hydrobiologia 67: 193-6.
Likens GE. 1983. A priority for ecological research. Bulletin of the Ecological Society of America 64(4): 234-43.
Likens GE. 1998. The Value of Long-term Data for Understanding Ecosystem Structure and Function: The Hubbard Brook example. Research in the Taieri Catchment. Occasional Paper No. 1, Ecology Research Group, University of Otago, pp. 2-4.
*Maloney RF. 1995. Effect of the herbicide triclopyr on the abundance and species composition of benthic aquatic macroinvertebrates in the Ahuriri River, New Zealand. New Zealand Journal of Marine and Freshwater Research 29: 505-15.
Marshall JW, Winterbourn MJ. 1979. An ecological study of a small New Zealand stream with particular reference to the Oligochaeta. Hydrobiologia 65: 199-208.
Maxted JR, Barbour MT, Gerritsen J, Poretti V, Primrose N, Silvia A, Penrose D, Renfrow R. 2000. Assessment framework for mid-Atlantic coastal plain streams using benthic macroinvertebrates. Journal of the North American Benthological Society 19: 128-44.
*Maxted JR, Evans BF, Scarsbrook MR. 2003. Development of standard protocols for macroinvertebtrate assessment of soft-bottomed streams in New Zealand. New Zealand Journal of Marine and Freshwater Research 37: 793-807.
*Maxted JR, McCready CH, Scarsbrook MR. 2005. Effects of ponds on stream water quality and macroinvertebrate communities. New Zealand Journal of Marine and Freshwater Research 39: 1069-84.
McBride GB. 2005. Using Statistical Methods for Water Quality Management: Issues, problems and solutions. Hoboken, New Jersey, USA: John Wiley and Sons Inc, 313 p.
Ministry for the Environment. 1997. Environmental Performance Indicators: Proposals for air, fresh water and land. Signposts for sustainability. Wellington: Ministry for the Environment, 158 p + appendices.
Norris RH, Norris KR. 1995. The need for biological assessment of water quality: Australian perspective. Australian Journal of Ecology 20: 1-6.
*Parkyn S, Davies-Colley RJ. 2003. Riparian management: how well are we doing? Water and Atmosphere 11(4): 15-17.
*Parkyn SM, Davies-Colley RJ, Halliday NJ, Costley KJ, Croker GF. 2003. Planted riparian buffer zones in New Zealand: do they live up to expectations? Restoration Ecology 11(4): 436-47.
Plafkin JL, Barbour MT, Porter KD, Gross SK, Hughes RM. 1989. Rapid Bioassessment Protocols for Use in Streams and Rivers: Benthic macroinvertebrates and fish. Washington DC: US Environmental Protection Agency, Office of Water Regulations and Standards.
*Quinn JM, Boothroyd LKG, Smith BJ. 2004. Riparian buffers mitigate effects of pine plantation logging on New Zealand streams. 2: invertebrate communities. Forest Ecology and Management 191: 129-46.
*Quinn JM, Cooper AB, Davies-Colley RJ, Rutherford JC, Williamson RB. 1997a. Land use effects on habitat, water quality, periphyton, and benthic invertebrates in Waikato, New Zealand, hill-country streams. New Zealand Journal of Marine and Freshwater Research 31: 579-97.
*Quinn JM, Cooper AB, Stroud MJ, Burrell GP. 1997b. Shade effects on stream periphyton and invertebrates: an experiment in streamside channels. New Zealand Journal of Marine and Freshwater Research 31(5): 665-83.
*Quinn JM, Hickey CW. 1990. Characterisation and classification of benthic invertebrate communities in 88 New Zealand rivers in relation to environmental factors. New Zealand Journal of Marine and Freshwater Research 24: 387-409.
*Quinn JM, Williamson RB, Smith RK, Vickers ML. 1992. Effects of riparian grazing and channelisation on streams in Southland. 2: benthic invertebrates. New Zealand Journal of Marine and Freshwater Research 26: 259-73.
Resh VH, McElravy EP. 1993. Contemporary quantitative approaches to biomonitoring using benthic macroinvertebrates. In: Rosenberg DM, Resh VH (eds) Freshwater Biomonitoring and Benthic Macroinvertebrates, pp. 159-194. New York and London: Chapman and Hall.
*Riley RH, Townsend CR, Niyogi DK, Arbuckle CA, Peacock KA. 2003. Headwater stream response to grassland agricultural development in New Zealand. New Zealand Journal of Marine and Freshwater Research 37: 389-403.
Rutherford JC. 1985. Some thoughts on trend analysis. In: Pridmore RD, Cooper AB (eds) Biological Monitoring in Freshwaters: Proceedings of a seminar, pp. 39-53. Wellington: National Water and Soil Conservation Authority.
*Scarsbrook MR, Boothroyd IKG, Quinn JM. 2000a. New Zealand's national river water quality network: long-term trends in macroinvertebrate communities. New Zealand Journal of Marine and Freshwater Research 34(2): 289-302.
*Scarsbrook MR, Quinn JM, Boothroyd IKG. 2000b. New Zealand's national river quality network − Reply: a balanced approach to interpretation of data. New Zealand Journal of Marine and Freshwater Research 34(4): 746-9.
*Scarsbrook MR, Halliday J. 1999. Transition from pasture to native forest land-use along stream continua: effects on stream ecosystems and implications for restoration. New Zealand Journal of Marine and Freshwater Research 33(2): 293-310.
*Scott D, White JW, Rhodes DS, Koomen A. 1994. Invertebrate fauna of three streams in relation to land use in Southland, New Zealand. New Zealand Journal of Marine and Freshwater Research 28: 277-90.
Smith DG, McBride GB, Bryers GG, Wisse J, Mink DFJ. 1996. Trends in New Zealand's national river water quality network. New Zealand Journal of Marine and Freshwater Research 30(4): 485-500.
Snelder TH, Biggs BJF. 2002. Multiscale river environment classification for water resources management. Journal of the American Water Resources Association 38(5): 1225-39.
Snelder T, Biggs B, Weatherhead M. 2004. New Zealand River Environment Classification Guide. NIWA report prepared for the Ministry for the Environment, 145 p.
*Stark JD. 1985. A macroinvertebrate community index of water quality for stony streams. Water and Soil Miscellaneous Publication 87: 53 p. Wellington: National Water and Soil Conservation Authority.
*Stark JD. 1993a. Ammonia-urea plant biomonitoring - is it defensible? In: Boyce W, Ericksen N, Hingley N (eds) Proceedings of the Regional Resource Futures Conference, Hamilton (27-29 August 1991), pp. 343-50. University of Waikato: Centre for Environmental and Resource Studies.
*Stark JD. 1993b. Performance of the Macroinvertebrate Community Index: effects of sampling method, sample replication, water depth, current velocity, and substratum on index values. New Zealand Journal of Marine and Freshwater Research 27: 463-78.
*Stark JD. 1998. SQMCI: a biotic index for freshwater macroinvertebrate coded abundance data. New Zealand Journal of Marine and Freshwater Research 32: 55-66.
Stark JD, Boothroyd IKG, Harding JS, Maxted JR, Scarsbrook MR. 2001. Protocols for Sampling Macroinvertebrates in Wadeable Streams. New Zealand Macroinvertebrate Working Group Report No. 1. Prepared for the Ministry for the Environment. Sustainable Management Fund Project No. 5103, 57 p. http://www.cawthron.org.nz/coastal-freshwater-resources/downloads.html
*Stark JD, Fowles CR. 2006. An Approach to the Evaluation of Temporal Trends in Taranaki State of the Environment Macroinvertebrate Data. Prepared for Taranaki Regional Council. Cawthron Report No. 1135, 88 p.
*Stark JD, Maxted JR. 2004. Macroinvertebrate community indices for Auckland's soft-bottomed streams and applications to SOE reporting. Prepared for Auckland Regional Council. Cawthron Report No. 970. Nelson: Cawthron Institute. ARC Technical Publication 303, 59 p. http://www.arc.govt.nz/arc/environment/water/publications/publications_home.cfm#ecology
*Stark JD, Maxted JR. 2007. A biotic index for New Zealand's soft-bottomed streams. New Zealand Journal of Marine and Freshwater Research 41(1).
*Stark JD, Moore SC, Berry A. 1999. Biotic indices: their role in water management in New Zealand. In: New Zealand Macroinvertebrate Working Group (eds) The Use of Macroinvertebrates in Water Management. Wellington: Ministry for the Environment, pp. 43-67.
*Storey RG, Cowley DR. 1997. Recovery of three New Zealand rural streams as they pass through native forest remnants. Hydrobiologia 353: 63-76.
*Suren AM, Biggs BJF, Duncan MJ, Bergey EA, Lambert PW. 2003. Benthic community dynamics during summer low-flows in two rivers of contrasting enrichment. 2: invertebrates. New Zealand Journal of Marine and Freshwater Research 37: 71-83.
Suren A, Snelder T, Scarsbrook M. 1998. Urban Stream Habitat Assessment Method (USHA). NIWA Client Report No. CHC98/60, 63 p + appendices.
Towns DR. 1985. Life history patterns and their influence on monitoring invertebrate communities. In: Pridmore RD, Cooper AB (eds) Biological monitoring in freshwaters: proceedings of a seminar, Hamilton, 21-23 November 1984. Water and Soil Miscellaneous Publication 83: 225-39.
Taranaki Catchment Commission. 1984. Freshwater Biology: Taranaki ring plain water resources survey. Stratford: Taranaki Catchment Commission, 196 p + appendices.
*Taranaki Regional Council. 2003. Taranaki − Our Place, Our Future: Report on the state of the environment of the Taranaki region. Stratford: Taranaki Regional Council, 206 p.
United States Environmental Protection Agency. 2006. Draft Wadeable Streams Assessment: A collaborative survey of the nation's streams. Report No. EPA 841-B-06-002. Washington DC: USEPA Office of Water, 82 p + appendices.
Vant B, Smith P. 2004. Trends in River Water Quality in the Waikato Region, 1987-2002. Environment Waikato Technical Report 2004/02. http://www.ew.govt.nz/publications/technicalreports/documents/TR04-02.pdf
Verneaux V, Verneaux J, Schmitt A, Lovy C, Lambert JC. 2004. The Lake Biotic Index (LBI): an applied method for assessing the biological quality of lakes using macrobenthos: the Lake Chalain (French Jura) as an example. Annales de Limnologie - International Journal of Limnology 40(1): 1-9.
Washington HG. 1984. Diversity, biotic and similarity indices: a review with special reference to aquatic ecosystems. Water Research 18: 653-94.
*Winterbourn MJ. 1999. Monitoring for sustainable river ecosystem management and the role of macroinvertebrates. In: The Use of Macroinvertebrates in Water Management: Recommendations of the New Zealand Macroinvertebrate Working Group. Wellington: Ministry for the Environment, pp. 1-15.
Winterbourn MJ, Alderton P, Hunter GG. 1971. A biological evaluation of organic pollution in the lower Waimakariri River system 1970-71. New Zealand Marine Department Fisheries Technical Report 67: 1-69.
Winterbourn MJ, Gregson KLD. 1981. Guide to the aquatic insects of New Zealand. Bulletin of the Entomological Society of New Zealand 9: 80 p.
*Winterbourn MJ, Gregson KLD, Dolphin CH. 2006. Guide to the aquatic insects of New Zealand (4th ed). Bulletin of the Entomological Society of New Zealand 14: 108 p.
Winterbourn MJ, Stark AW. 1978. A biological survey of the Kaiapoi River following fellmongery effluent treatment. Mauri Ora 6: 11-21.
*Wright-Stow AE, Winterbourn MJ. 2003. How well do New Zealand's stream-monitoring indicators, the Macroinvertebrate Community Index, and its quantitative variant, correspond? New Zealand Journal of Marine and Freshwater Research 37: 461-70.