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A sewer was a cavernous tunnel and pipe system through which effluent and excess storm water flowed away from the inhabitants of a city.
Missy and Clara explored a sewer beneath a Dalek city on Skaro. Missy explained to Clara that the sewers' primary function was not to house the Daleks' waste, but instead to house decomposing, used Dalek mutants. This was because Daleks were genetically engineered to not die naturally.
The Twelfth Doctor later tricked Davros in his own plan. He used his regeneration energy to strengthen the dying Dalek matter and bring it back to full health. The mutants from the sewers then rose up and attacked the overcity. (TV: The Witch's Familiar)