Endogenous nitrogen pollution can be a major cause of eutrophication. Nitrogen species release from sediments can be reduced by biologically-enforced zeolite mulch or water column aeration. This study was about their combined effects. Water and surface sediment samples from the Yangzhou ancient canal were aerated and biozeolite mulching was applied separately and in combination for 81 days, while the nitrogen species removal rate was recorded. The combination of aeration and biozeolite mulching removed >95% of the ammoniacal-nitrogen in 15 days. This was better than either the blank control or biozeolite mulch without aeration. The ammoniacal-nitrogen concentration was lowered faster by combined treatment than by aeration alone. Nitrate nitrogen was only detected during aeration between days 10 and18, and reached lower concentration in the presence of biozeolite. Nitrate was formed during aeration but its concentrations were higher and more variable in the absence of biozeolite; that is, mulching stabilized nitrate formation. The total nitrogen concentration reached its lowest levels after 81 days with biozeolite treatment alone, with 78% total nitrogen removal, whereas combined aeration with biozeolite achieved 41%. This shows that biozeolite mulching can remove nitrogen in eutrophic waters, even without aeration.