The　effects　of　free　ammonia　(FA)　or　free　nitrous　acid　(FNA)　on　partial　nitrification　(PN)　has　been　well　investigated.　Nevertheless,　little　information　was　known　about　the　combined　effects　of　nitrogen　loading　rate　(NLR)　and　substrate　inhibition,　as　well　as　the　impact　on　the　community　structure　of　nitrifiers.　In　this　work,　real　reject　water　was　treated　in　a　pre-denitrification　reactor.　PN　was　achieved　by　gradually　increasing　NLR,　and　it　was　successfully　maintained　when　average　FA　and　FNA　were　within　0.8-3.2　mg　NH3-N/L　and　0.003-0.067　mg　HNO2-N/L,　respectively.　When　NLR　was　reduced,　PN　was　slightly　affected　due　to　the　FA　declination.　As　FNA　inhibition　was　also　eliminated　by　adding　alkalinity　into　the　influent,　PN　was　completely　destroyed　quickly.　FISH　results　indicated　the　deterioration　of　the　PN　was　mainly　attributed　to　the　recovery　of　NOB　when　inhibition　effects　were　limited.　It　concluded　the　increase　of　NLR　benefited　the　partial　nitrification.　However,　the　stability　of　the　nitrite　path　way　was　more　dependent　on　selective　substrate　inhibition　effects,　especially　the　FNA　inhibition.　These　findings　would　be　important　for　further　treatment　of　actual　reject　water.