Many modern ships have toilets where the effluent is treated biologically - lots of bacteria munch away at it before overboard discharge - so that all effluent is sterile and doesn't pollute the water. They work pretty much the same as the septic tank in my yard. The process takes some time though, and ships have enough capacity to process large amounts of waste.
Biological toilets wouldn't be practical in aeroplanes. Weight constraints alone, prevent us keeping the waste aboard long enough for the bacteria to do their job. So, we download the raw sewage at the end of the flight and cart it off to septic tanks, where the bacteria can relax and digest the stuff at their leisure.
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Through difficulties to the cinema