In spite of all efforts to avoid and recycle, the large volume of goods produced at the chemical park nevertheless generates non-reusable waste, including among others sewage sludge. This is thermally processed in a waste incineration plant. The process steam generated by the incineration plant is fed into the central steam grid and is used in downstream production processes. The incineration plant for sewage sludge is also used by the surrounding communities, including Altötting and Burgkirchen; about 70% of the incinerated sewage sludge originates from the municipalities.

Incineration is not possible for small volumes of the waste generated at the chemical park; this includes excavated soil and unavoidable production waste. These materials are deposited in environmentally compatible ways in on-site landfills on the grounds of the GENDORF Chemical Park. In total, the GENDORF Chemical Park has three landfills – two landfills are active, while one landfill was closed in 1996.