There can be several types of unwanted substances in wastewater. Some of the substances among these can be highly toxic and need to be removed during the process of wastewater treatment. Many of them can be organic materials, alkalies, acids etc. Minerals such as zinc, mercury, silver, lead, cadmium, thallium, copper, chromium, selenium, arsenic etc. can also be present in varying concentrations in wastewater which, for example, comes from industries ranging from manufacturing to textiles. Some of these substances may not be harmful in small concentrations (trace amounts) but higher concentrations can be very toxic.

Different processes can be used to remove such toxic chemicals treatment from wastewater. Biological treatment processes, though very effective in general wastewater treatment, are ineffective for removal of toxic chemicals from wastewater. Removal of such toxic chemicals treatment substances is usually part of the tertiary phase of wastewater treatment.

One way to remove metals from wastewater is by precipitating the metals out using metal scavengers. This is assisted by changing the water pH or with chemicals such as sodium mono-sulfide or sodium poly-sulfides or sodium hydrogen sulfide which assist in forming flocs (precipitates) which contain the metal ions. These flocs can be removed from wastewater by filtration.  Apart from that microfiltration or diatomaceous filtration systems can be used for removal of heavy metals from wastewater. In this method, a crucial part of the equipment includes a membrane which is impervious to solid metal particles. However, it may not be so effective if the metals are in dissolved form in the wastewater. The filtered water (called filtrate), thus, obtained can be further subjected to reverse osmosis process for further polishing. Metal ions can also be selectively removed from wastewater by adsorption. Among others, carbonaceous adsorbents such as commercial lignin, carbon soot and commercially available carbon can be used for adsorption of metal ions from wastewater. Commercial lignin, for example, can adsorb chromium ions and cautions of zinc and lead. Loading rates, pH, etc. can affect the adsorption process efficiency.

Ion exchange is another effective method that helps in reduction of heavy metal concentration in wastewater. In this method a cationic or anionic solid insoluble ion exchange resin with harmless metal ions is applied in wastewater. The soluble toxic heavy metal ions are transferred to the solid resin while the harmless metal ions that were initially present on the solid ion exchange resin are transferred to wastewater. An advantage of this process is that it can help in selectively removing certain heavy metal ions. For example, the positively charged ions (for example, hydrogen or sodium ions) present on cationic resins can be exchanged with positively charged ions in wastewater. These can be, for example, nickel, copper or zinc ions. On the other hand, negatively charged ions such as chloride or hydroxyl ions present on anionic resins can be exchanged selectively with negatively charged ions. These can be, for example, chromate, sulfate, cyanide, nitrates and even dissolved organic carbon that is present in wastewater. These resins can then be harnessed and heavy metal ions can be regenerated into solution from them in a controlled environment for eventual removal. This way, the resins, now being freed of heavy metal ions, can be reused.

Advanced oxidation process another method which is very useful for treating wastewater containing toxic non-degradable substances such as pesticides, aromatic substances, petroleum products and volatile organic products (VOCs). This process removes dissolved toxic organic substances by oxidation using hydroxyl radicals and thus incinerating them within the wastewater. Ozone, hydrogen peroxide, UV light are used in such processes to oxidize and remove toxic chemicals treatment from wastewater. Therefore, this process is also called in situ chemical oxidation. Although, the advanced oxidation processes (AOPs) are very effective in removal of any toxic organic compounds in aqueous phase, the costs involved in such processes can be high.

Many technologies which use the above processes are now available and can be used depending on specific needs.