This paper presents an experimental study focusing on the effect of intake pipe blockage on the critical submergence of lateral dual square intakes under perpendicular uniform approach flow. The pipe blockage is implemented by various intake protrusions into the approach flow, with one of the intakes always kept flush with the channel sidewall. An increase in protrusion of downstream intake alone causes a significant decrease in critical submergence, and an increased protrusion of upstream intake alone causes higher critical submergence when both intakes operate under identical conditions. At higher protrusions of twice the intake size, the mutual influence between the intakes was negligible with multiple vortex formations at both intakes in dual configuration. Based on the results, an empirical equation is proposed for the computation of critical submergence for lateral dual protruded intakes and was found to be in good agreement with the experimental results, which will be useful in the design for fixing the invert level of dual intakes under approach flow condition. The flow blockage due to protrusion can be adopted effectively to reduce the critical submergence for multiple intake structures.