Water hammer phenomenon is an important consideration in designing of many hydraulic systems due to extreme variations in pressure it causes. For example, the dramatic pressure rise can cause pipes to rupture. Accompanying the high pressure wave, there is a negative wave that can cause very low pressures leading to the possibility of contaminant intrusion or column separation. This paper investigates the effect of different parameters such as fluid density, steady flow velocity, air entrainment, pipeline material type and pipeline friction factor on transient flow in pipeline system due to pump shut down, effect of protection devices on the transient pressure head along the pipeline and effect of existence of a crack in pipeline flow. WHAMO software was used in the analysis which uses the implicit finite difference scheme for solving the momentum and continuity equations at unsteady state case. The study was applied on a pipeline composed of six segments of different diameters and elevations with a total length of 2523 m. The flow is pumped in the pipeline by pumping station to a constant head reservoir at the end of the pipeline. The results showed that many parameters such as fluid density, steady flow velocity, air entrainment, pipeline material type and pipeline friction factor have significant effect on the water hammer phenomenon. Also, it was found that in spite of the non-return valve protects the pump from water hammer effect, increases the pressure head in the pipeline. Surge tank or air chamber fitted at the beginning of the pipeline can protect it effectively from the water hammer effect. At the end, it was found that a crack in pipeline can cause intrusion from outside the pipe to inside and inversely can cause leakage to outside or both.