This article examined long-term effects of using navigation tools on wayfinding and spatial orientation, through a survey analysis of the experience of using navigation tools and spatial aptitudes, and a behavioral experiment of real-world navigation. Experience of tool use was measured in terms of regular use (time length and frequency) and accumulated experience (time length multiplied by frequency). The survey analysis showed that frequent users of pedestrian navigation systems tended to be low on sense of direction and mental rotation. In contrast, longtime users of maps tended to be high on sense of direction and favor survey navigation strategies. The behavioral experiment showed that people who had more accumulated experience of using in-car navigation systems traveled less efficiently and learned the configurations of traveled routes less accurately with a mobile tool and a paper map. The analysis of long-term effects through structural equation modeling showed that spatial aptitudes and accumulated experience of tool use independently affect wayfinding and spatial orientation and that the negative effects of accumulated experience were larger than the positive effects of spatial aptitudes. The results and implications are discussed in relation to existing studies of short-term effects and spatial thinking.