The design of hydrokinetic plants in hydropower canals involves the choice of the array layout, rotor geometry, turbine spacing, and array spacing, and necessitates the control of the resultant backwater to avoid upstream flooding hazards. Several works in the literature have shown that array power optimization is feasible with small spacings between the arrays, disregarding the limitation in the power output induced by backwater upstream. In this study, a 1-D channel model with a Double Multiple Streamtube code and wake sub-models are integrated to predict an array layout that will maximize the array power. The outputs of the conducted sensitivity analysis confirm that this design enabled improved power conversion with closely spaced turbines and largely spaced arrays, thus allowing for a partial recovery of the total head variation for a new array deployed upstream. In addition to the quantitative assessment of the mechanical power converted, the tool enables depth control from the downstream undisturbed flow station to the backwater exhaustion far upstream, thereby increasing its flexibility. Furthermore, it overcomes the limitations of actuator disc models by considering rotor’s fluid dynamic losses. The results show that power output linearly scales for a limited number of arrays (≤5), whilst the variation in water depth variation follows a power law from the most downstream array towards upstream, regardless of the plant size. Finally, the maximum upstream inflow depth is demonstrated to become asymptotic for large multi-array plants under ideal conditions.