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保(bao)(bao)護(hu)區于1997年(nian)經(jing)江西省人民政(zheng)府批(pi)建為(wei)省級(ji)自(zi)然保(bao)(bao)護(hu)區，歸屬南昌市管(guan)理，后經(jing)過5年(nian)科考和3年(nian)申報，于2008年(nian)1月由(you)國(guo)務院批(pi)準為(wei)國(guo)家級(ji)自(zi)然保(bao)(bao)護(hu)區，并(bing)更名為(wei)“鄱陽湖南磯濕地國(guo)家級(ji)自(zi)然保(bao)(bao)護(hu)區”。
行政上隸屬南(nan)(nan)昌(chang)市(shi)新建縣(xian)南(nan)(nan)磯鄉(xiang)，距(ju)南(nan)(nan)昌(chang)市(shi)城區約60公里(li)。保護(hu)(hu)區東至(zhi)(zhi)太子河入東湖口、西(xi)至(zhi)(zhi)贛江中支下游，北至(zhi)(zhi)三山(shan)腳，南(nan)(nan)至(zhi)(zhi)磯山(shan)以(yi)(yi)(yi)南(nan)(nan)鳳(feng)尾湖，東西(xi)寬21.6公里(li)，南(nan)(nan)北寬27.7公里(li)，范圍基本與南(nan)(nan)磯鄉(xiang)行政邊界(jie)(jie)一致。保護(hu)(hu)區是江西(xi)省(sheng)面(mian)積(ji)較(jiao)大(da)的河口類型國家級保護(hu)(hu)區，緊鄰省(sheng)會南(nan)(nan)昌(chang)。地理坐標(biao)在東經116°10′～116°25′，北緯(wei)28°51′～29°08′之間(jian)。東界(jie)(jie)以(yi)(yi)(yi)10個拐(guai)(guai)(guai)點(dian)(dian)(dian)(dian)的連線為界(jie)(jie)，拐(guai)(guai)(guai)點(dian)(dian)(dian)(dian)的坐標(biao)分別(bie)為（116°18′57″E，29°06′52″N）；南(nan)(nan)界(jie)(jie)沿余干縣(xian)縣(xian)界(jie)(jie)向西(xi)南(nan)(nan)至(zhi)(zhi)拐(guai)(guai)(guai)點(dian)(dian)(dian)(dian)（116°17′50″E，28°51′59″N）；西(xi)界(jie)(jie)以(yi)(yi)(yi)（116°17′50″E，28°51′59″N）為起點(dian)(dian)(dian)(dian)，沿南(nan)(nan)昌(chang)縣(xian)縣(xian)界(jie)(jie)向北至(zhi)(zhi)大(da)車荒，再經16個拐(guai)(guai)(guai)點(dian)(dian)(dian)(dian)至(zhi)(zhi)北界(jie)(jie)起點(dian)(dian)(dian)(dian)（116°09′51″E，29°06′11″N），拐(guai)(guai)(guai)點(dian)(dian)(dian)(dian)的坐標(biao)分別(bie)為（116°16′10″E，28°56′16″N）；北界(jie)(jie)以(yi)(yi)(yi)9個拐(guai)(guai)(guai)點(dian)(dian)(dian)(dian)的連線為界(jie)(jie)，拐(guai)(guai)(guai)點(dian)(dian)(dian)(dian)的坐標(biao)分別(bie)為（116°10′22″E，29°07′8″N)。
南磯自然保(bao)護區(qu)在第四紀(ji)以來的(de)地(di)質構造運動（新構造運動）中處于中心沉(chen)降區(qu)，因此(ci)它也(ye)是不斷發育(yu)的(de)各古(gu)河流水(shui)系(xi)的(de)匯聚中心。南磯自然保(bao)護區(qu)具有“二元結構”的(de)沖積—沖洪積相網紋紅土(tu)(tu)(tu)、砂(sha)礫(li)石堆積，構成了厚(hou)達30～75m的(de)沉(chen)積地(di)層。在更(geng)新世沉(chen)積地(di)層或白堊系(xi)紫紅色粉砂(sha)巖基巖上，全新世沉(chen)積由(you)(you)下而上，顆粒變(bian)細，下部(bu)(bu)為礫(li)卵石、砂(sha)礫(li)石、砂(sha)（含礫(li)）組成的(de)粗(cu)碎(sui)屑(xie)(xie)，層面清晰，磨圓度(du)和(he)分選(xuan)性較好，上部(bu)(bu)則主要(yao)由(you)(you)亞粘(zhan)土(tu)(tu)(tu)、亞砂(sha)土(tu)(tu)(tu)等夾不穩定淤泥質薄層組成的(de)細碎(sui)屑(xie)(xie)。
南(nan)磯自然保護區內河(he)(he)道(dao)(dao)數目眾多，大小河(he)(he)道(dao)(dao)有50條(tiao)左右，河(he)(he)道(dao)(dao)長(chang)短不一(yi)，形態各(ge)異，而且由于沖淤作用(yong)還使(shi)得河(he)(he)道(dao)(dao)形態處于進(jin)一(yi)步的(de)發育和變化之中。最長(chang)河(he)(he)道(dao)(dao)達22.57km，最短也有1.08km，河(he)(he)道(dao)(dao)總長(chang)度為123.53km。
鄱(po)(po)陽湖(hu)區屬亞(ya)熱(re)帶(dai)暖濕季(ji)風區，一年內冬(dong)季(ji)和(he)(he)東南季(ji)風進退交換(huan)和(he)(he)西太平(ping)洋副熱(re)帶(dai)高壓南北振動，對鄱(po)(po)陽湖(hu)流(liu)域(yu)的(de)天氣(qi)變(bian)化和(he)(he)氣(qi)候形(xing)成(cheng)產生重大影響(xiang)，決定(ding)了氣(qi)候的(de)周期(qi)性變(bian)化。一般冬(dong)季(ji)極地大陸(lu)冷氣(qi)團向南流(liu)動，由于南移的(de)路(lu)徑不同，或西北路(lu)，或西路(lu)南下(xia)影響(xiang)鄱(po)(po)陽湖(hu)區，形(xing)成(cheng)每年3～4次的(de)寒潮天氣(qi)，使湖(hu)區寒冷少雨，或出現雨雪天氣(qi)。
該保護區總面(mian)(mian)積33300公(gong)頃，其中核(he)心區面(mian)(mian)積17500公(gong)頃，緩沖區面(mian)(mian)積5500公(gong)頃，實驗區面(mian)(mian)積10300公(gong)頃。
鄱陽湖南磯自然保護(hu)區(qu)植(zhi)物(wu)(wu)(wu)(wu)物(wu)(wu)(wu)(wu)種(zhong)(zhong)豐(feng)富(fu)，區(qu)系成(cheng)分復雜(za)，類型多樣，顯示具(ju)(ju)有(you)(you)明顯的(de)南北植(zhi)物(wu)(wu)(wu)(wu)匯合的(de)過渡(du)性質(zhi)。濕地植(zhi)物(wu)(wu)(wu)(wu)雖具(ju)(ju)有(you)(you)地帶性“烙印”，但隱域(yu)性特征明顯。據統計，保護(hu)區(qu)共有(you)(you)維管束植(zhi)物(wu)(wu)(wu)(wu)115科(ke)(ke)(ke)304屬443種(zhong)(zhong)，其(qi)中(zhong)(zhong)蕨類植(zhi)物(wu)(wu)(wu)(wu)11科(ke)(ke)(ke)11屬12種(zhong)(zhong)，裸子(zi)植(zhi)物(wu)(wu)(wu)(wu)5科(ke)(ke)(ke)10屬11種(zhong)(zhong)，被子(zi)植(zhi)物(wu)(wu)(wu)(wu)99科(ke)(ke)(ke)283屬420種(zhong)(zhong)。蓼科(ke)(ke)(ke)（Polygonaceae 16種(zhong)(zhong)）、薔(qiang)薇科(ke)(ke)(ke)（Rosaceae 17種(zhong)(zhong)）、豆科(ke)(ke)(ke)（Leghminosae 23種(zhong)(zhong)）、菊(ju)科(ke)(ke)(ke)（Composifae 31種(zhong)(zhong)）、禾本科(ke)(ke)(ke)（Graminae 24種(zhong)(zhong)）、莎草科(ke)(ke)(ke)（Cyperaceae 22種(zhong)(zhong)）等6科(ke)(ke)(ke)在(zai)本區(qu)具(ju)(ju)有(you)(you)明顯優勢，占有(you)(you)主導(dao)地位(wei)，對本區(qu)植(zhi)被的(de)構成(cheng)、動態和區(qu)系組成(cheng)具(ju)(ju)有(you)(you)重要作(zuo)用。研究區(qu)中(zhong)(zhong)的(de)苔草群(qun)落(luo)(luo)Cares spp. Comm.、蘆葦群(qun)落(luo)(luo)Phragmites australis Comm.、眼子(zi)菜群(qun)落(luo)(luo)Potamogeton spp. Comm.、蓼群(qun)落(luo)(luo)Polygonum spp. Comm.、針(zhen)藺群(qun)落(luo)(luo)Eleocharis spp. Comm.等世界廣布種(zhong)(zhong)是該區(qu)域(yu)的(de)主要建(jian)群(qun)種(zhong)(zhong)。中(zhong)(zhong)國特有(you)(you)屬在(zai)本區(qu)內僅有(you)(you)3個栽培植(zhi)物(wu)(wu)(wu)(wu)屬，即(ji)：水(shui)杉屬Metasequoia、枳屬Poncirus、南天竹屬Nandina。自然分布植(zhi)物(wu)(wu)(wu)(wu)中(zhong)(zhong)無中(zhong)(zhong)國特有(you)(you)植(zhi)物(wu)(wu)(wu)(wu)屬，此與(yu)濕地植(zhi)被的(de)典型隱域(yu)性質(zhi)有(you)(you)關。
2003-2004年保(bao)(bao)護(hu)區(qu)(qu)(qu)綜合科(ke)學考察統計到浮游(you)動(dong)物(wu)(wu)(wu)62屬111種(zhong)(zhong)(zhong)(zhong)，底棲(qi)動(dong)物(wu)(wu)(wu)8科(ke)62種(zhong)(zhong)(zhong)(zhong)，水生(sheng)昆(kun)蟲11目(mu)(mu)(mu)(mu)(mu)40科(ke)168種(zhong)(zhong)(zhong)(zhong)，魚(yu)(yu)類(lei)6目(mu)(mu)(mu)(mu)(mu)14科(ke)43屬58種(zhong)(zhong)(zhong)(zhong)，其(qi)中江湖(hu)洄(hui)游(you)型魚(yu)(yu)類(lei)占40%，兩棲(qi)動(dong)物(wu)(wu)(wu)1目(mu)(mu)(mu)(mu)(mu)5科(ke)11種(zhong)(zhong)(zhong)(zhong)，爬行動(dong)物(wu)(wu)(wu)3目(mu)(mu)(mu)(mu)(mu)10科(ke)23種(zhong)(zhong)(zhong)(zhong)，哺乳動(dong)物(wu)(wu)(wu)7目(mu)(mu)(mu)(mu)(mu)12科(ke)22種(zhong)(zhong)(zhong)(zhong)。特別地(di)，南磯保(bao)(bao)護(hu)區(qu)(qu)(qu)是具有(you)科(ke)研(yan)、保(bao)(bao)護(hu)與(yu)觀賞價值的濕(shi)地(di)生(sheng)態系統和濕(shi)地(di)鳥(niao)(niao)類(lei)保(bao)(bao)護(hu)區(qu)(qu)(qu)，區(qu)(qu)(qu)內鳥(niao)(niao)類(lei)種(zhong)(zhong)(zhong)(zhong)類(lei)多，數量大，目(mu)(mu)(mu)(mu)(mu)前記錄到15目(mu)(mu)(mu)(mu)(mu)45科(ke)205種(zhong)(zhong)(zhong)(zhong)，有(you)鸊鷉目(mu)(mu)(mu)(mu)(mu)2種(zhong)(zhong)(zhong)(zhong)，鵜形(xing)(xing)(xing)目(mu)(mu)(mu)(mu)(mu)1種(zhong)(zhong)(zhong)(zhong)，鸛形(xing)(xing)(xing)目(mu)(mu)(mu)(mu)(mu)17種(zhong)(zhong)(zhong)(zhong)，雁(yan)形(xing)(xing)(xing)目(mu)(mu)(mu)(mu)(mu)25種(zhong)(zhong)(zhong)(zhong)，隼形(xing)(xing)(xing)目(mu)(mu)(mu)(mu)(mu)10種(zhong)(zhong)(zhong)(zhong)，雞形(xing)(xing)(xing)目(mu)(mu)(mu)(mu)(mu)2種(zhong)(zhong)(zhong)(zhong)，鶴形(xing)(xing)(xing)目(mu)(mu)(mu)(mu)(mu)12種(zhong)(zhong)(zhong)(zhong)，鸻形(xing)(xing)(xing)目(mu)(mu)(mu)(mu)(mu)25種(zhong)(zhong)(zhong)(zhong)，鷗形(xing)(xing)(xing)目(mu)(mu)(mu)(mu)(mu)7種(zhong)(zhong)(zhong)(zhong)，鴿形(xing)(xing)(xing)目(mu)(mu)(mu)(mu)(mu)3種(zhong)(zhong)(zhong)(zhong)，鵑形(xing)(xing)(xing)目(mu)(mu)(mu)(mu)(mu)6種(zhong)(zhong)(zhong)(zhong)，鸮形(xing)(xing)(xing)目(mu)(mu)(mu)(mu)(mu)5種(zhong)(zhong)(zhong)(zhong)，佛法僧目(mu)(mu)(mu)(mu)(mu)6種(zhong)(zhong)(zhong)(zhong)，鴷形(xing)(xing)(xing)目(mu)(mu)(mu)(mu)(mu)2種(zhong)(zhong)(zhong)(zhong)，雀形(xing)(xing)(xing)目(mu)(mu)(mu)(mu)(mu)82種(zhong)(zhong)(zhong)(zhong)。其(qi)中，濕(shi)地(di)水鳥(niao)(niao)共7目(mu)(mu)(mu)(mu)(mu)89種(zhong)(zhong)(zhong)(zhong)，占中國水鳥(niao)(niao)種(zhong)(zhong)(zhong)(zhong)類(lei)的35.6%。保(bao)(bao)護(hu)區(qu)(qu)(qu)內不同季節里鳥(niao)(niao)類(lei)種(zhong)(zhong)(zhong)(zhong)類(lei)組成差異顯著，冬季鳥(niao)(niao)類(lei)142種(zhong)(zhong)(zhong)(zhong)，春季鳥(niao)(niao)類(lei)120種(zhong)(zhong)(zhong)(zhong)，夏季鳥(niao)(niao)類(lei)58種(zhong)(zhong)(zhong)(zhong)，秋季鳥(niao)(niao)類(lei)64種(zhong)(zhong)(zhong)(zhong)。
由于地(di)處贛江、鄱陽湖(hu)和(he)(he)長(chang)江的關鍵節點(dian)，保護區(qu)具有良好的通(tong)江性,不僅是鯉、鯽等(deng)經濟魚(yu)類的重(zhong)要產卵和(he)(he)育肥場(chang)所(suo)，也是長(chang)江中下游(you)地(di)區(qu)青(qing)、草、鰱(lian)、鳙、鰻鱺(li)、刀鱭、鳳尾魚(yu)等(deng)洄(hui)游(you)型魚(yu)類的主要洄(hui)游(you)通(tong)道甚至是避難所(suo)，對于鄱陽湖(hu)、贛江和(he)(he)長(chang)江漁業資(zi)源保護與可持(chi)續利用具有重(zhong)要意義。保護區(qu)典型的入湖(hu)口濕(shi)地(di)生(sheng)態(tai)系(xi)統，是河口自然(ran)地(di)理、水文和(he)(he)生(sheng)態(tai)環境監測等(deng)學科的天然(ran)研(yan)究基地(di)，是研(yan)究內陸河口濕(shi)地(di)生(sheng)態(tai)系(xi)統的場(chang)所(suo)。
