Sixty “Mega Cities” would emerge by 2015 catering of 600 million populations, and were threatened by the climate change, because of cyclones, flooding, etc. Jakarta became a metro region covering Jakarta, Bogor, Tangerang, Bekasi, Depok and Cianjur. Jakarta metropolitan faced the very high population growth, urban sprawling, traffic jams, flooding, green open space reduction, environmental degradation, urban slums and illegal street hawkers. Flooding and traffic congestions were the two most important issues to solve.SWOT analysis and urban design solutions were produced to create a sustainable solution. Related to transportation issues, Singapore Mass Rapid Transport (MRT) concept was evaluated. Meanwhile the Netherlands’ polder concept as well as Singapore’s Integrated Water Management were also analyzed.The development of above ground MRT as well as Busway could be developed to connect Jakarta Metropolitan Region. The networks were developed on the main toll road networks. The MRT and Busway would eventually replace the need of automobile use in the future. The Transit – Oriented – Development (TOD) with high density can be suggested to be concentrated nearby the MRT and Busway interchange stations. The Netherlands’ polder and were adopted for urban’ low-lying lands in Jakarta Metropolitan Region, A polder system was defined as the Integrated Man-made Drainage System consisting Dikes, Drains, Retention Ponds, Outfall Structures or Pumping Stations. The polder system was proposed to be extended to Tangerang and Bekasi area.