This is a very simple question: Why are oxidized compounds generally thought to be less toxic/polluting than reduced species? This is used in waste water treatment where oxidizing agents (such as chlorine) are added to remove organic AND inorganic pollutants.
Generally, there are rather few (by mass) unpolar compounds in a biologic system. They are often bioactive (steroids, terpenes, etc.) and/or toxic. Coming from nonbiologic source, they are very often toxic.
Once they've been partially oxidised (as in "added oxygen", "made more polar", not as in "chlorinated"), there are much more possibilities for further metabolic breakdown. Polar substances don't usually (exceptions prove the rule) survive terribly long in nature, because some thing or other finds them nutritious. ;-)
Of course the intermediate metabolites can be even more toxic (it's often a metabolism that was "meant" by nature to do sth else), and it doesn't work out all the time, but the general trend is clear: keep oxidising, and you end up with CO2 and water. The smaller and more polar the fragments become, the quicker.
And one comment on chlorinating: Improperly done, esp. on dirty water, it produces organochlorides, which are practically all toxic. The modern way is to clean the water with excess ozone, and then add a tiny amount of hypochloride (if necessary, i.e. in warm countries or if the piping is not in good working order) to the pure water, to keep the water pipes from moulding. It's just to kill any microorganism that tries to sneak back in, not to actually oxidise him.
And for inorganic compounds: Underground water very often contains soluble iron and manganese (II), because the inside of our earth is generaly a bit reductive. They are removed by bubbling air through the water, the rapidly oxidised +3 ions then precipitate on a sand filter. Chlorination would do the same, but so does ozone, if you really need a very rigourous workup (e.g. surface water). I guess using chlorine is a 1960ies technology. We visited our local water station when I was in primary school in the 80ies, and I remember they explained it as "like in your municipal swimming pool".
There is not such as general/ic rule but water treatment has used, waste water as inflow. It is not as we are discussing the oxidation of X to obtain Y, if you get the point. The target is to get an outflow of water that can be reused or discharged in nature without significant impact. The lines below do not pertain to the treatment of industrial wastes nor the removal of a specific pollutant. Normally no toxic compounds go to the sink, and even in the lab we are not supposed to flush chemicals down.
Oxidative processes in waste water treatment mainly consists of biological aerobic ones, basically the demolition of a wide range of chemicals as it would naturally occur in a natural environment by means of bacterial activity.
What is peculiar here is that the waste water is kept in a regulated physical and chemical environment able to sustains and ease the process (for instance the oxygen required by the microorganisms is guaranteed by injecting air, or the temperature is regulated, ecc.).
This aerobic biological oxidation is targeting biodegradable pollutants is not targeting any specific chemical. Again, keep in mind that we are speaking of waste water not of special industrial waste. Even a chemical toxic to the bacteria, or in other words interfering with the bacterial metabolism, does not pose a limitation as far is getting degraded in the while.
Most of the organic pollutants are decomposed into carbon dioxide and water leaving a water with high content of nitrites, nitrates, phosphates that must be lowered in subsequent steps and is full of particulate and biomass that must be separated as well.
Let assume all the steps above have resulted in a sufficiently clear and relatively pure water, then yes a chemical oxidation is performed. This step might use chlorinated chemicals and other oxidizers, but it is just targeting the residual microorganisms and tailored just to do that, like in the case of the disinfection of a swimming pool. It is performed when virtually there is nothing to oxidize but the residual organisms that were at the start of the whole treatment.