As rainfall becomes scarcer or more erratic, we rely more on irrigation systems for agricultural and human water provision. Impacts of irrigation canals such as the barrier effect on wildlife movements are poorly documented. Although canal culverts and overpasses can be used by wildlife, little is known about their crossing behavior to guide barrier effect mitigation efforts. Over seven years, we recorded medium-sized carnivore crossings by video-surveillance through 30 culverts and 28 overpasses in a large irrigation project in south-central Portugal. We examined the influence of the structures’ features and landscape context on the likelihood of canal crossing. Culvert crossings were positively influenced by the proportion of nearby montado, a high nature value farming system. Overpass crossings were more likely in areas away from paved roads and with more nearby wetlands. Overpasses increased the crossing rates by about 11% relative to culverts and both were crossed more often in landscapes with evenly distributed land uses. In the project area, 20% of the montado has recently transitioned to irrigated agriculture, and wetlands have increased by 43%. It is therefore plausible that the increase in the crossing rate of overpasses relative to culverts will be accentuated. Our study produced the first evidence of a contrast in crossing rates among irrigation canal crossing structures. We have shown that the landscape can be a driver of animal crossings but irrigation projects can in turn be transformative of the landscape. Broadly, the fact that the deployment of irrigation canals may favor some land uses over others creates a conundrum that needs careful consideration when planning barrier effect mitigation interventions.