We theoretically demonstrate the generation of ultrashort isolated attosecond pulses (IAPs) in the water window region with a multi-cycle inhomogeneous two-color field synthesized by an 800-nm fundamental pulse and a 2000-nm control pulse. The results show that the high-order harmonic generation process is effectively controlled in the temporally and spatially shaped field. An ultra-broadband supercontinuum in the water window region with the photon energies ranging from 387 to 620 eV is generated. Such a supercontinuum supports the generation of an ultrashort IAP with a duration as short as 40 attosecond. Moreover, we analyze the influence of the carrier-envelope phases (CEPs) and the relative phase of the two-color field on the IAP generation. It is shown that our two-color scheme is robust for the generation of sub-80 as IAPs against variations of the CEPs and the relative phase.