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Spatial navigation involves the use of various cues. This study examined how cue conflict influences navigation by contrasting landmarks and optic flow. Participants estimated spatial distances under different levels of cue conflict: minimal conflict, large conflict, and large conflict with explicit awareness of landmark instability. Whereas increased cue conflict alone had little behavioral impact, adding explicit awareness reduced reliance on landmarks and impaired the precision of spatial localization based on them. To understand the underlying mechanisms, we tested two cognitive models: a Bayesian causal inference (BCI) model and a non-Bayesian sensory disparity model. The BCI model provided a better fit to the data, revealing two independent mechanisms for reduced landmark reliance: increased sensory noise for unstable landmarks and lower weighting of unstable landmarks when landmarks and optic flow were judged to originate from different causes. Surprisingly, increased cue conflict did not decrease the prior belief in a common cause, even when explicit awareness of landmark instability was imposed. Additionally, cue weighting in the same-cause judgment was determined by bottom-up sensory reliability, while in the different-cause judgment, it correlated with participants’ subjective evaluation of cue quality, suggesting a top-down metacognitive influence. The BCI model further identified key factors contributing to suboptimal cue combination in minimal cue conflicts, including the prior belief in a common cause and prior knowledge of the target location. Together, these findings provide critical insights into how navigators resolve conflicting spatial cues and highlight the utility of the BCI model in dissecting cue interaction mechanisms in navigation.