<p>The Shichika irrigation canal, extending over the alluvial fan of the Tedori River in Ishikawa Prefecture, Japan, has a series of tilting weirs and drops, which potentially hinder fish migration. Owing to its connection to the sea, 11 diadromous fish species have been found in the canal. However, no reports exist of upstream migration modeling of fish considering the number of hydraulic drops and tilting weirs, validated by passive integrated transponder (PIT) tag observation in agricultural canals. We aimed to estimate the influence of tilting weirs on fish migration along a canal. A computational model was developed to simulate the upstream migration of <i>Ayu (Plecoglossus altivelis</i>), a representative species of migratory fish. The developed model was calibrated based on biotelemetric observations using PIT tags in the Yamajima irrigation canal, a branch of the Shichika irrigation canal. The model consists of 2 sub-models: channel and drop sections. In the channel section, <i>Ayu</i> was assumed to swim along the channel based on the characteristics of the swimming duration curve. In the drop section, <i>Ayu</i> was assumed to decide whether to swim or jump upstream, based on a comparison of the velocity of the falling water and its burst speed. The computational results were validated using the observed time required to pass through the 2 PIT tag antennas. Furthermore, using the identified swimming ability parameters of <i>Ayu</i>, a significant effect of the conditions of tilting weirs on the upstream migrations of <i>Ayu</i> was demonstrated by simulation through the canal of 3.5&#xa0;km.</p>