In the current global warming and sea level rise,frequent occurrence of waterlogging and salt water intrusion exists in the worldwide estuarine and coastal cities. The relative sea level rise is dozens or even hundreds of times the absolute sea level rise in these areas. Complex effect of absolute sea level rise,tectonic subsidence,land subsidence by the groundwater extraction in the coastal cities, scour depth caused by the human intervention in the river catchment of Changjiang River (Yangtze River) as Three Gorges Dam, rise of water level and depth datum led by the land reclamation and deep waterway regulation has been estimated from the point of view of the continuous system consisted of river catchment, estuary and coastal sea in the present paper. The results show that: (1) The absolute sea level rise is 2. 0mm/a (2011 ~2030). It is an average value of the results analyzed from the annually averaged sea level in the records at the Wusong gauge station (1912 ~2000) using a combined linear regression analysis integrated with grey system with wavelet analysis proposed by the authors, and using the least square method integrated with wavelet analysis. (2)The tectonic subsidence is cited 1mm/a (2011 ~2030),the measured by the very long baseline interferometer(VLBI) in 1990s. (3) Land subsidence is cited as 4mm/a(2011 ~2030) predicted in 1996. (4) Scour depth of the estuarine channel is estimated at 2 ~10cm (2011 ~ 2030) and the rise of water level is estimated at 8 ~ 10cm (2011 ~2030) . Therefore, the relative sea level rise (RSLR) will be speculated about 10~16cm (2010~2030) in the Shanghai City. The RSLR will lead to the rise of tidal level 8 ~24cm,the rise of tidal current 2 ~20cm/s,the rise of design high tidal level 16cm and the rise of design wave height 12. 48cm, respectively, for the coastal defense in the coming 20 years. The RSLR will also reduce the flood control standard and adaptive action should be implemented as the partition fortification as the improvement of seawall standard to meet 200 years plus 12 level wind along the coastline of mainland and Changxing Island, to meet once in 100 years with 11 levels of winds along the coastline of Chongming Island and Hengsha Island, and gradually heightening and strengthening and implementing key beach protection and emergency protection plan. Impacts of sea level rise on the fresh water supply in three reservoirs named Chenhang, Qingcaosha, and Dongfengxisha are simulated by our three-dimensional hydrodynamic and temperature and salinity model of the Changjiang Estuary with the adjacent waters in dry season runoff guarantee rate at Datong station. Six indicators of the impacts are guaranteed rate of water intake, the longest continuous days with no water, intake water quality and supply water quality,intake water quantity and supply water quantity. Simulated results show that three reservoirs will be affected. To this end, the action guideline to the sea level rise strategy in the Shanghai City have been proposed to the Shanghai government as (1) recent actions (2012~2015) to upgrade the city water supply and drainage engineering and protective engineering; (2) interim actions (2016~ 2020) to improve sea level monitoring and early warning system,and then the special,city, regional planning considering sea level rise ; (3) long term actions (2021 ~2030) to implement both the safety and the transformation and development of the city.