The channel migration or shifting of navigable river channels have been an issue of major concern, as their effects on the transport environment, channel corridors, the manoeuvrability of vessels transiting these channels and vessels navigation amongst other factors result to inefficiency in inland transport in the riverine region of Ilaje, Nigeria. Most navigational and operational challenges have been attributable to alterations in the waterway channel due to aggradation and degradation processes in the river regime. The study’s goal is to explore channel migration along the Igbokoda-Ayetoro waterway with a view to provide mitigation methods to address potential difficulties along the waterway channel and in the adjoining environment. The objectives of the study include gathering satellite imagery of the study area between 1972 and 2022; assessing the morphological planforms of the study river channel, and assessing the river channel’s effective width using the segment-transect method. The study considered channel width, depth and alignment as indicators to be carefully evaluated to ensure safe, sustainable and efficient inland navigation measures. To ascertain the shapes and forms of the channel during the study period, geospatial and computer-aided techniques were used. Channel widths were extracted using the Segment-Transect method at 100-meter intervals. 50 year and 100-year estimate of the extent of channel/banklines shifting were determined. According to the study, there are changes in the channel’s width, depth and planform (alignment) that make the waterway indeterminate and unsuitable for vessels transiting on two-way manoeuvrability lanes. Hence, the study recommended the sustainable mitigation strategies to tackle the potential challenges pose by channel migration and reduce its impact on the vessel manoeuvrability, navigation and the adjoining environment.