This paper takes a novel approach towards designing and managing the architecture and operating protocol of injection/production system. The shut-in valve positioning and timing of valve closure control the amplitude and frequency of pressure waves generated during shutdowns. The proposed approach provides the means for mitigating the negative impact of water hammer on the integrity of the near wellbore region and provides an idea of the intensity of any cross-flow issues. It is based on a comprehensive model that examines the fast wellbore transients (water hammer) generated by routine or emergency shutdown of injector or producer wells, which can also cause interaction with a near wellbore region of reservoir. The modeling handles the coupling of the conventional transient pipe flow hydraulics with the transient reservoir flow. The decompression wave created by shutting down an injector interacts with the near wellbore region that induces a transient flow back from the reservoir which creates a risk of mechanical damage by dislodging and transporting material with the fluid movement and even result in sand production. The compression wave created by shutting down a producer may induce repeated injection pulses. In both producing and injection cases, multiple cross-flow phenomena can be triggered between formation layers and wells interconnected within the injection or production system. The analyses of these transient phenomena help to potentially quantify the mechanical damage, which may be induced in near wellbore reservoir region, and assess the potential damage risk associated with produced solids.