Mishrif carbonate formation is widely developed in Iraq and other areas of Middle East. When it comes to carbonate reservoir water injection development, the high heterogeneity commonly existed in carbonate reservoirs makes water flow complicated and performance of water injection differed from reservoir to reservoir. The existence of high permeability stripes and zones would make the problem more complicated and always result water early break through and poor sweep of the reservoir. Water injection pilots started recently in Mishrif carbonate reservoirs in M Field and N Field in southern Iraq. The objectives of these pilots were to investigate the feasibility to conduction water flooding in the Mishrif carbonate reservoirs, including test the injectivity and its change through time, sweep efficiency, responses from offset producers, investigate the methods that can be applied to tackle the problems brought by high permeability zones in water injection. The pilots were carried out in two different well patterns in the two fields, one is inverted nine spots pattern and the other is vertical-horizontal well pattern with vertical well as injector. In one pilot, separated injection was applied to avoid water channeling and improved producer performance. 3D numerical model was applied to track and monitor water sweep during the pilot. It was found out that directional connectivity and high permeability zones were developed in these reservoirs and resulted in early water breakthrough and quick increase of water cut in offset producers. This effect impact vertical and lateral sweep greatly and lower recovery potential in future field water flooding development if not well learned and handled. The challenges are to make description of these directional connectivity and distribution of high permeability zones in reservoir description and modeling and find effective ways in field operations to avoid the negative impact of them in field scale water flooding. To tackle the challenges, integrated reservoir study of multi-discipline is necessary in order to make full description of high permeability zones and reservoir heterogeneity and understand their mechanism on water sweep. It is suggested to pay additional attention to high permeability zone as a key factor in reservoir development of these kinds of reservoirs and integrated the study results into the design of field development plan in an early stage, to narrow the uncertainties brought by them and reduce development risks.