My view is that if we protect the natural mechanism for self-purification of water, it will save a part of our effort and energy in doing technological treatment / cleaning of water.
To protect the natural mechanism, we need to know it better.
The results of our studies of the mechanism (applying what I called 'inhibitory analysis') are in the papers, which are presented at the sites:
1.    Ostroumov S. A. The concept of aquatic biota as a labile  and vulnerable component of the water self-purification system - Doklady Biological Sciences, Vol. 372, 2000, pp. 286–289. http://sites.google.com/site/2000dbs372p286biotalabil/;
2.    Ostroumov S. A.,  Kolesnikov M. P. Biocatalysis of Matter Transfer in a Microcosm Is Inhibited by a Contaminant: Effects of a Surfactant on Limnea stagnalis. - Doklady Biological Sciences, 2000,  373: 397–399. Translated from Doklady Akademii Nauk, 2000, Vol. 373, No. 2, pp. 278–280. http://sites.google.com/site/2000dbs373p397biocatallstag/
3.    Ostroumov S. A. An aquatic ecosystem: a large-scale diversified bioreactor with a water self-purification function.- Doklady Biological Sciences, 2000. Vol. 374, P. 514-516.  http://sites.google.com/site/2000dbs374p514bioreactor/
4.    Ostroumov SA. Criteria of ecological hazards due to anthropogenic effects on the biota: searching for a system. - Dokl Biol Sci (Doklady Biological Sciences). 2000; 371:204-206. http://sites.google.com/site/2000dbs371p204criteria/
5.    Ostroumov S. A. An amphiphilic substance inhibits the mollusk capacity to filter out phytoplankton cells from water. - Biology Bulletin, 2001, Volume 28, Number 1, p. 95-102.
     Biology Bulletin: ISSN    1062-3590 (Print) 1608-3059 (Online); DOI    10.1023/A:1026671024000; http://www.springerlink.com/content/l665628020163255/;
6.    Ostroumov S. A. Inhibitory Analysis of Regulatory Interactions in Trophic Webs. -Doklady Biological Sciences, 2001, Vol. 377, pp. 139–141. Translated from Doklady Akademii Nauk, 2000, Vol. 375, No. 6, pp. 847–849. [In the paper, the author developed a new approach to analyze the fundamental ecological issue, the interactions between organisms in ecosystems. He suggested to use the methodology of  inhibitory analysis to study interactions in trophic chains. Important situation is the top–down control of plankton by benthic filter-feeders. This control, as author’s experiments have shown, might be removed by chemical inhibitors (the latter may enter the ecosystem as pollutants)]. http://sites.google.com/site/2001dbs377p139inhibitory/; http://blog.researchgate.net/masterblog/299_Inhibitory_Analysis_A_new_method_for_analyzing_interactions_between_organisms_in_ecosystems;
7.    Ostroumov SA. The synecological approach to the problem of eutrophication. - Dokl Biol Sci. (Doklady Biological Sciences). 2001; 381:559-562. http://scipeople.com/uploads/materials/4389/Danbio6_2001v381n5.E.eutrophication.pdf
8.    Ostroumov SA. The hazard of a two-level synergism of synecological summation of anthropogenic effects. - Dokl Biol Sci. (Doklady Biological Sciences).  2001; 380:499-501. http://sites.google.com/site/2001dbs380p499synerg/ 
9.    Ostroumov SA. Responses of Unio tumidus to mixed chemical preparations and the hazard of synecological summation of anthropogenic effects.  - Dokl Biol Sci (Doklady Biological Sciences). 2001; 380: 492-495. http://sites.google.com/site/2001dbs380p492unio/
10.    Ostroumov SA, Kolesnikov MP. Pellets of some mollusks in the biogeochemical flows of C, N, P, Si, and Al. - Dokl Biol Sci (Doklady Biological Sciences). 2001; 379:378-381. http://sites.google.com/site/2001dbs379p378pellets/
11.    Ostroumov SA. Imbalance of factors providing control of unicellular plankton populations exposed to anthropogenic impact. - Dokl Biol Sci (Doklady Biological Sciences). 2001; 379:341-343. http://sites.google.com/site/1dbs379p341imbalance/; https://www.researchgate.net/profile/Sergei_Ostroumov/blog/321_Discovery_of_the_system_where_chemical_pollution_could_impair_the_regulation_and_balance_in_the_abundance_of_phytoplankton_threat_to_ecological_stability_  [posted 20 Dec 2009]
12.     Ostroumov SA. Effect of amphiphilic chemicals on filter-feeding marine organisms.-  Dokl Biol Sci (Doklady Biological Sciences). 2001; 378:248-250. For the first time, oysters were used as the test-organisms in bioassay of synthetic surfactants and detergents.  The new data revealed a novel type of hazard to mariculture. New negative effects of surfactants and chemical mixtures on water filtering activity of Crassostrea gigas were discovered. http://sites.google.com/site/2001dbs378p248effammaroyst/
13.    Ostroumov SA. Biodiversity protection and quality of water: the role of feedbacks in ecosystems. -  Dokl Biol Sci (Doklady Biological Sciences). 2002; 382:18-21; http://sites.google.com/site/2dbs382p18biodivers/; http://www.citeulike.org/pdf/user/ATP/article/6113559/ostroumov_02_biodiversity.pdf;
14.    Ostroumov S. A. Identification of a New Type of Ecological Hazard of Chemicals: Inhibition of Processes of Ecological Remediation. - Doklady Biological Sciences, Vol. 385, 2002 (November), pp. 377–379. [Translated from Doklady Akademii Nauk, Vol. 385, No. 4, 2002, pp. 571–573]. https://www.researchgate.net/file.FileLoader.html?key=8408a7cfaa984764b812ce79c77007f2;
15.    Ostroumov S.A. Anthropogenic effects on the biota: towards a new system of principles and criteria for analysis of ecological hazards. - Rivista di Biologia/Biology Forum. 2003.  96: 159-170.  Review.  PMID: 12852181 [PubMed - indexed for MEDLINE] http://sites.google.com/site/ostroumovsergei/publications-1/rivista2003criteria
16.    Ostroumov S. A. On the biotic self-purification of aquatic ecosystems: elements of the theory. - Doklady Biological Sciences, 2004, Vol. 396, Numbers 1-6, p. 206-211. https://www.researchgate.net/file.FileLoader.html?key=60f338228d6f3c5114d223ab81e15d3b;  https://www.researchgate.net/profile/Sergei_Ostroumov/blog/348_Useful_theory_of_natural_mechanisms_of_improving_water_quality;
17.    Ostroumov S. A.,  Widdows J.  Inhibition of mussel suspension feeding by surfactants of  three classes. // Hydrobiologia. 2006. Vol. 556, No. 1. Pages: 381 – 386. 3 Tables. Bibliogr. 37 refs. [For the first time the negative effects of the three surfactants on the filtration rates by marine mussels were presented in one paper. The xenobiotics tested represented anionic, cationic and non-ionic surfactants (tetradecyltrimethylammonium bromide, TDTMA, a representative of a class of cationic surfactants; sodium dodecyl sulphate, SDS, a representative of anionic alkyl sulfates; and Triton X-100, a representative of non-ionic hydroxyethylated alkyl phenols). Negative effects of SDS, TDTMA, and Triton X-100 on the filtration activity of marine mussels M. edulis and M. edulis / M. galloprovincialis were discovered. All three surfactants inhibited the clearance rates. This is the first publication of the negative effects of a cationic surfactant on Atlantic mussels Mytilus. The significance of the results for the ecology of marine ecosystems is discussed]. DOI 10.1007/s10750-005-1200-7; http://sites.google.com/site/ostroumovsergei/publications-1/hydrobiologia2006ostwidd; http://sites.google.com/site/3surfactantsfiltrationmytilus/; http://scipeople.ru/uploads/materials/4389/_Hydrobiologia2006%20vol%20556%20No.1%20pages381-386.pdf; http://www.springerlink.com/content/7166067538534421/
18.    Ostroumov S. A. Biotic self-purification of aquatic ecosystems: from the theory to ecotechnologies. - Ecologica, 2007. vol. 15 (50), p.15-23. (ISSN 0354-3285). Some basic elements of a new theory for the biological mechanism for water self-purification are presented. Hydrobionts (aquatic organisms) are actively involved in various processes leading to water purification. Not only microorganisms (bacteria, cyanobacteria and fungi), but also algae, plants, invertebrates, and many other groups of organisms are involved, which is discussed and analyzed in the paper. Results of the author's experiments that study the effects of various pollutants on aquatic organisms (freshwater and marine bivalves) are given. The theory is an innovative basis for developing ecological technologies to clean water and to upgrade its quality by using organisms and ecosystems [http://scindeks.nb.rs/article.aspx?artid=0354-32850750015O].
19.    Ostroumov S.A., Shestakova T.V. Decreasing the measurable concentrations of Cu, Zn, Cd, and Pb in the water of the experimental systems containing Ceratophyllum demersum: The phytoremediation potential // Doklady Biological Sciences 2009, Vol. 428, No. 1, p. 444-447. http://sites.google.com/site/9dbs444/; https://www.researchgate.net/file.FileLoader.html?key=8fd8998627b86102db72c9b237c25054;
20.    Ostroumov S.A. Towards  the general theory of ecosystem-depended control of water quality. - Ecologica, 2009, vol. 16, No. 54, p. 25-32. (Faculty of Biology, Moscow State University, Leninskie Gory, Moscow, 119991 Russia). Abstract:  A new set of ecological generalizations formulated in this paper represent, in a systematized form, the basic elements of the qualitative theory of biotic control of water quality and water self-purification in freshwater and marine ecosystems.  The theory contributes to a better understanding of the issues of stability and regulation in the biosphere. The theory is supported by the results of the author’s experimental studies of the effects exerted by surfactants, detergents and other pollutants on  aquatic organisms.http://sites.google.com/site/9enecologica16p25theory/

Some of the publications above and the results in them won some awards and Diplomas, including:
Diploma at the 1st International Forum on Conservancy of Nature (Moscow, 7-9th September 2005), signed by Co-Chairs of the Forum, Deputy Minister of Natural Resources of Russian Federation and Vice-President of the Trade Chamber of Russian Federation). 
Diploma of the journal 'Ecology and Life' (awarded 15 October 2005).
Diploma of the competition 'Sustainable use of natural resources and environmental protection – stratery of sustainable development of Russia in the 21st century' at the international conference 'Sustainable Development: Nature-Society-Man' (organized in 2006, Moscow,  by the Ministry of Natural Resources) for the paper by Ostroumov S.A. and Solomonova E.A. "On studies of water self-purification and interactions between pollutants (surfactants) and biota: searching approaches to issues relevant to sustainable use of water resources " (Directive of the Ministry of Natural Resources No.126 of 02 June 2006; the Diploma was signed by the Minister).
Diploma to the book 'Biotic Mechanism of Self-purification of Freshwater and Marine Water' by Dr. S. A. Ostroumov, awarded at the 7th International Conference ‘Aquatic Ecosystems, Organisms, Innovations’ (2005). Diploma of the Academy of Aquatic Sciences for the series of innovative publications on aquatic ecology, interactions between chemicals and organisms, and water self-purification, including the books 'Biological Effects of Surfactants in Connection with the Anthropogenic Impact on the Biosphere'; 'Biological Effects of Surfactants on Organisms'; 'Biotic Mechanism of Self-Purification of Freshwater and Marine Water'; 'Pollution, Self-Purification and Restoration of Aquatic Ecosystems'; 'Biological Effects of Surfactants', (awarded in 2006).
Diploma of the Academy of Aquatic Sciences 'for his innovative contribution to improvement of environmental and ecological education', including the book 'Ecology and Hydrobiology. Curricula of  Lecture Courses' (awarded in 2006).
Diploma of the Moscow Society of the Researchers of Nature (awarded in 2007).

FULL TEXTS OF SOME OF THE PUBLICATIONS see at:
http://blog.researchgate.net/masterblog/299_Inhibitory_Analysis_A_new_method_for_analyzing_interactions_between_organisms_in_ecosystems;
https://www.researchgate.net/profile/Sergei_Ostroumov/blog/347_Biodiversity_and_stability_of_ecosystems;
http://blog.researchgate.net/masterblog/276_New_threat_to_water_quality_discovery_of_the_new_important_type_of_hazards_from_pollution_Synecological_summation_of_effects_on_different_trophic_levels;
http://blog.researchgate.net/masterblog/255_Criteria_of_ecological_hazards_due_to_anthropogenic_effects_on_the_biota_Searching_for_a_system;
http://blog.researchgate.net/masterblog/262__The_Concept_of_Aquatic_Biota_as_a_Labile_and_Vulnerable_Component_of_the_Water_SelfPurification_System;
http://blog.researchgate.net/masterblog/241_innovative_concept_of_ecosystem_as_a_multifunctional_bioreactor_one_of_its_functions_is_upgrading_water_quality_ecosystem_service;
http://blog.researchgate.net/masterblog/180_A_new_type_of_effect_of_potentially_hazardous_substances

http://sites.google.com/site/2000dbs371p204criteria/
http://sites.google.com/site/2000dbs373p397biocatallstag/
http://sites.google.com/site/2000dbs374p514bioreactor/
http://sites.google.com/site/2001dbs379p378pellets/
http://sites.google.com/site/2001dbs377p139inhibitory/
http://sites.google.com/site/2001dbs378p248effammaroyst/
http://sites.google.com/site/2001dbs380p499synerg/ 
http://sites.google.com/site/2001dbs380p492unio/
http://sites.google.com/site/2dbs382p18biodivers/;
http://sites.google.com/site/bioeffectsofsurfactants/
http://sites.google.com/site/surfactantinhibitfilterfeed02/
http://sites.google.com/site/3surfactantsfiltrationmytilus/
http://sites.google.com/site/9dbs444/;
https://www.researchgate.net/file.FileLoader.html?key=8fd8998627b86102db72c9b237c25054;
http://scipeople.com/uploads/materials/4389/Danbio6_2001v381n5.E.eutrophication.pdf;

ADDITIONAL REFERENCES OF RELEVANT PUBLICATIONS see:
http://sites.google.com/site/ostroumovsergei/
http://sites.google.com/site/bioticupgradewaterquality2008/
http://sites.google.com/site/ostroumovsa/
http://sites.google.com/site/biochemicalecology/
http://sites.google.com/site/ostroumovsapublicationsineng/
http://sites.google.com/site/ostroumovsapublicationsruen/
http://sites.google.com/site/ostroumovsergei/publications-that-cited-saostroumov
http://sites.google.com/site/biosphereostroumov/home
http://sites.google.com/site/ecologytobemostcitedtomorrow/home
http://sites.google.com/site/ecologytobemostcitedtomorrow/list-of-publications-by-sa-ostroumov
http://scipeople.ru/users/2943391/
https://www.researchgate.net/profile/Sergei_Ostroumov/blog/321_Discovery_of_the_system_where_chemical_pollution_could_impair_the_regulation_and_balance_in_the_abundance_of_phytoplankton_threat_to_ecological_stability_ [posted 20 Dec 2009];