However, the above answers have focused on reducing or stopping pollution sources, but also reduce the consumption of water from the river has played an important role.
Given the dilution effect of higher river discharges, the rate of pollutants is reduced.
Thus, enhancement and protection of the environmental flows level can lead to river restoration.
The most cost effective way are the use of Ozone in the river system. Oxidize on several areas portion of the water and release it back in to the River. Soon beneficial Algae will start growing and other beneficial bacteria and vertebrate will return to the River system. This kind of treatment is very effective where the river is affected by organic human and animal waste.
Most important is to stop the pollution source first or at least to diminish it, maybe by pretreatment. The following steps depend from the local situation that I don't know. But I guess you know all this anyway.
I would ask you to look at the EU Water Framework Directive. It focuses on returning rivers to there natural state. They use rivers as exemplars that are in there natural state then attempt to return poor rivers to a comparable state.
I would again state that the EU WFD is an ideal piece of reading for this question
I agree with Dr Hoffman, the first thing that needs to be done is to prevent/reduce pollution of rivers and give them a chance to recoup.
I have helped develop a cost effective method of reducing the impact of liquid effluents using microbes and advanced filtration and aeration systems. Our first unit with a capacity of treating 250 cubic metres of effluents is being installed shortly in Indonesia. We will be progressively increasing the capacity of our equipment in the next few months. This equipment is capable of converting effluent to clean water and we can possibly bring it to drinking water standards if required.
A unit of this capacity will cost less than USD 50,000 and operating costs will be about 25 cents per cubic metre or lower. If such units can be installed in sufficient numbers, the rivers can return to their naturla state.
However, you have to know the criteria you want to reach at the "originally ecosystem". It is quite difficult to bring it back to the "natural state" if you do not know what normally was there, or how much or how many of natural resource group you want to bring back. Then, you can measure whether you get close to the original state or not.
Firstly any pollution sources will be stopped or extremely reduced by treatment of waste water discharges and all other human degradation should be avoided (water pumping, dams, solid discharges...)
To stop pollution requires at first that we change our behavior in regard to our environmental living space, which requires on the other hand a lot of Money because where humans are living there is waste produced. The easy way we go that we dump in the rivers and streams which on the other hand is then responsible for all kind of diseases and sickness which again then needs medical care and is another source of costs. Today not only a big problem for developing Countries but as well for the developed Countries. Environmental awareness is a mind set which can be achieved only when People having a proper education, enough Money to feed their families and understand the impact pollution are having on their lives. The years in environmental consultancy has proven and shown that there is no easy solution to pollution. It costs Money and it needs education and all of that is missing on a global and wide scale.
We have developed an Twin Injector oxidation unit with high capacity which comes with an 6kw Diesel Generator for the costs of 12.000USD and ideal suited for remote villages but as well for lakes, streams and Rivers, with the generator we generate energy which can be used as well for Radio and light so People wi have access to information how to make life more comfortable when we take care of nature where we are part of it.
Based on the turnover time or the time needed for the entire volume of a reservoir to be renewed, rivers only need 12-20 days to renew itself. But because of human intrusion (waste disposal, human settlement, factory sites, etc), pollution in rivers are increased. If it is possible in any way to eliminate these, then the river can naturally renew itself. One should also take note that rivers are resilient to these types of disturbances, thus they have the capability to go back to their original state even after a disturbance.
However, the above answers have focused on reducing or stopping pollution sources, but also reduce the consumption of water from the river has played an important role.
Given the dilution effect of higher river discharges, the rate of pollutants is reduced.
Thus, enhancement and protection of the environmental flows level can lead to river restoration.
First you have to describe what is the meaning of "the originality of a river ecosystem". What is the originality of "your River"? It is difficulty to bring some background values without know the originality . We have some indicators values as, for example, DO, turbidity, electric conductivity, phosphate, but that values are variable from sites (they are just "guide" values, not "correct " values). We have aquatic invertebrates that are possible to use as biondicators, but that aquatic community change from sites too. In my point of view, you can use a reference river from your region or hydrographic basin (from a preserved area) to turn possible use variables as "guide" values.
It is perhaps difficult sometimes rather impossible to put a river's original ecosystem, mean while a number of physical changes apart from sources of pollution could have cropped up as settlement expansion on both sides as we see in Delhi and elsewhere. The most important being dams. Even warnings of expert geophysicists and geologists could not deter the government to construct a huge Tehri Dam that made Ganga, when post monsoon comes to base level, a dirty ditch. Besides cropping practices and land cover could have changed to the level it would take a long period to reverse to a certain level of landscape improvement.
The first and main issues were already mentioned by Juliano Corbi and Mohammad F K.. The originality of a river could be its state 100 years ago or 1000 years ago and it comprises hydromorphological parameters. If you have bigger settlements along the river it will not be realistic to go back to originality.
The first that I would do, is to include the whole basin looking at point and non-point loads (using GIS) and to improve whatever is possible.
The next question is if you should change the hydromorphological state of the river itsself to improve longitudinal, traversal and vertical connectivity (giving more room to the river course, remove unnecessary dams, connect wetlands, buffer stripes etc.).
And finally, I also would firstly use bio-indicators to control if the ecological state is improving.