The main publication resulting from WBBS is the BTO's BirdTrends report, in which the survey's long-term trends are put into context alongside other monitoring of population levels and measures of breeding productivity and annual survival rates. The overall picture for each species is discussed using the recent scientific literature. BirdTrends is updated annually to take account of each year's new data and publications.

A series of BTO research reports details the planning and development of the WBBS and aspects of its results, for birds and for mammals. In addition, there are some peer-reviewed publications that have used WBBS data. Some key references are listed below, in date order:

Marchant, J.H., Langston, R. & Gregory, R.D. (1996) The Waterways Bird Survey: an evaluation and appraisal of its future role. R&D Technical Report W22. Environment Agency, Bristol. Full text

Langston, R.H.W., Marchant, J.H. & Gregory, R.D. (1997) Waterways Bird Survey: evaluation of population monitoring and appraisal of future requirements. In Freshwater Quality: defining the Indefinable? (eds Boon, P.J. & Howell, D.L.), pp 282–289. The Stationery Office & Scottish Natural Heritage, Edinburgh. ISBN: 0114957541

Marchant, J.H., Gregory, R.D., Balmer, D.E., Gough, S.J. & Wilson, A.M. (1998) A comparison of breeding bird numbers along canals with and without a close season for fishing. Research Report 211. BTO, Thetford.

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Marchant, J.H. & Gregory, R.D. (1999) Waterways Breeding Bird Survey pilot survey 1998: adaptation of BBS census methods to rivers and canals. R&D Technical Report W205. Environment Agency, Bristol. Full text

Marchant, J.H., Noble, D.G., Leech, D.I. &  Freeman, S.N. (2002) River Habitat Survey and Waterways Breeding Bird Survey 1998–2000: final report. R&D Technical Report W1-043/TR. Full text

Marchant, J.H. & Gregory, R.D. (2004) Surveying riparian breeding birds in the United Kingdom. In Bird Numbers 1995, Proceedings of the International Conference and 13th Meeting of the European Bird Census Council, Pärnu, Estonia, (ed Anselin, A.). Bird Census News 13 (2000): 19–31.

Vaughan, I.P. (2004) Development of species distribution models and their application to birds in river habitats. PhD thesis, Cardiff University. Full text

Newson, S.E., Noble, D.G. & Marchant, J.H. (2005) Waterways Breeding Bird Survey: preliminary analyses of mammal data 1998–2003.  Research Report 405. BTO, Thetford. ISBN 1-904870-41-4.

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Marchant, J.H., Joys, A.C., Noble, D.G. & Coombes, R.H. (2006) Waterways Breeding Bird Survey: progress and population trends 1998–2004. Science report SC010012. Environment Agency, Bristol. ISBN: 1844325334 Full text

Vaughan, I.P., Noble, D.G. & Ormerod, S.J. (2007) Combining surveys of river habitats and river birds to appraise riverine hydromorphology. Freshwater Biology 52: 2270–2284.

Everard, M. & Noble, D. (2010) The development of bird indicators for British fresh waters and wetlands. Aquatic Conservation: Marine and Freshwater Ecosystems 20: S117–S124. doi: 10.1002/aqc.1074

Royan, A., Hannah, D.M., Reynolds, S.J., Noble, D.G. & Sadler, J.P. (2013) Avian community responses to variability in river hydrology. PLoS ONE 8(12): e83221. Full text

Baillie, S.R., Marchant, J.H., Leech, D.I., Massimino, D., Sullivan, M.J.P., Eglington, S.M., Barimore, C., Dadam, D., Downie, I.S., Harris, S.J., Kew, A.J., Newson, S.E., Noble, D.G., Risely, K. & Robinson, R.A. (2014) BirdTrends 2014: trends in numbers, breeding success and survival for UK breeding birds. Research Report 662. BTO, Thetford.

Royan, A., Hannah, D.M., Reynolds, S.J., Noble, D.G. & Sadler, J.P. (2014) River birds' response to hydrological extremes: new vulnerability index and conservation implications. Biological Conservation 177: 64–73.

Royan, A., Prudhomme, C., Hannah, D.M., Reynolds, S.J., Noble, D.G. & Sadler, J.P. (2015) Climate-induced changes in river flow regimes will alter future bird distributions. Ecosphere 6 (4). 50. doi: 10.1890/ES14-00245.1