How about constructed wetlands. Microbes removes more than 80 %. It requires anaerobic and aerobic cycles that can be facilitated by proper hydraulic regime in the wetland.
I fully agree with Mowjood. A properly constructed wetland designed to fit the topography has these advantages:
a) Provides a high level of treatment - Properly designed, constructed, maintained and managed wetlands can provide very efficient treatment of animal wastewater. Test results show that phosphorus, nitrate-nitrites, ammonia, BOD5 and suspended solids can be reduced to very acceptable levels.
b) Is inexpensive to operate - A constructed wetland requires little, if any, energy use and equipment needs are minimal. A well-designed wetland transfers water by gravity through the system. If topography limits the use of gravity, pumps will be necessary which increases the cost of operation. Once established, properly designed and constructed wetlands are largely self-maintaining.
c) Can be relatively inexpensive to construct - Each constructed wetland's design is site specific, taking into consideration such variables as topography, water supply, soil types, type of livestock operation, etc. Selection of a site with accommodating specifications keeps establishment costs low.
d) Reduces, if not completely eliminates, odor - Odor is a serious problem when handling and treating animal wastewater, especially if the farming operation is located in close proximity to residential housing. Unlike lagoons, Ohio State University Extension research on three constructed wetlands in eastern Ohio has shown that odors from wetlands are of very low intensity or are non-existent.
e) Is able to handle variable wastewater loadings - Properly-designed wetlands have shown great tolerance for varying amounts of wastewater loading. This is important because varying livestock production levels, changing climatic conditions, and modifications in management can alter loading rates significantly.
f) Reduces the land area needed for application of wastewater - Constructed wetlands reduce the concentration of contaminants. Thus, the land area needed for application of water from a constructed wetland is less than the land area needed for direct application of wastewater.
g) Can be ascetically pleasing - Depending upon design, location, and type of vegetation, constructed wetlands can enhance the landscape with color, texture, and variety in plant materials.
h) Provide wildlife habitat - Wetlands attract some types of wildlife and can add to the usefulness and attractiveness of the area.
From the foregoing inputs, I have not seen any reference to the level of nitrate itself and I think that this would have been a good starting points from there we can select the most suitable technique.
The concept of wetlands and or the Point system are both attractive aiming at eliminating nitrate, but there is also the undesirable risk of contributing to green house gases emission (NO,N2O) as a result of incomplete reduction.
On the other hand we know that nitrogenous fertilizers (as well as PK) and irrigation water are key limiting elements in modern agriculture. Therefore from a recycling perspective knowing the total NPK in sewage water, it can reduce significantly agricultural reliance on NPK imports. Consequently recommendation for NPK fertilizers should be adjusted accordingly to avoid any unintended loading of crop land.
One may argue about the risk of deep seepage, therefore the rate and timing of application (soil type and crop) should be established beforehand in order not to unduly displace the ecological risk to agricultural land.