Hydrophytes effect directly canal performance by reducing water flow, enhancing sedimentation, raising water level and reduce canal cross section area. The free-floating hydrophytes trapped in the outlets and culverts dipping its flow. In this apprehension a research study was conducted to investigate the effects of hydrophytes on canal capacity and at the outlets on the performance of the secondary canal known as Yar Hussain Minor (YHM) of Maira branch canal; part of the upper Swat canal irrigation system in Khyber Pakhtunkhwa (KP) province of Pakistan. Maira branch canal and its secondary canals were designed for crop based irrigation operation (CBIO), which could supply irrigation water for maximum cropping intensity (180%) even during peak periods of irrigation requirements. The existing water allowance was 0.67 Ls-1 ha-1 (6.6 mm day-1), which was based on the maximum crop water requirements. The challenges faced by YHM are physical barriers like hydrophytes and the turbid water received from river Swat producing eutrophication, sedimentation and encourage further growth of hydrophytes. Moreover to control the flow of water for the outlets triangular profile crump’s weirs have been used in all secondary canals including YHM for comparative division to the tertiary outlets. Hydrophytes growth was observed in head reaches of canal. Five types of aquatic weeds were found. The hydrophytes growth in canal head reaches directly reduces the cross section by more than 50%. Indirectly the free-floating hydrophytes got stuck in the outlets and affected its flow. Therefore, daily discharges were measured with and without detached hydrophytes at each outlet from staff gauging. Frequency was based on days hydrophytes blockage observed divided by total time. It is concluded that the presence of hydrophytes decreased the performance of secondary canal, the hydrophytes and users’ interventions (like putting stones to affect flow) influenced the outlets performance by 80%. Furthermore trifurcators type outlets were more prone to influence by hydrophytes followed by bifurcators outlet.