As most pagodas were tall and stood erect and visible, they were used to pilot ships to harbors or mark ferry crossings on rivers. In ancient times pagodas were often located on river-banks, by sea harbors or near ferry crossings or bridges. These towering buildings could be seen from far away. Some pagodas have become symbolic marks for certain harbors or wharves. Luoxing Pagoda at Mawei Harbour in Fuzhou, Fujian Province, has long been recorded as an important navigation mark on world navigation maps. The famous Liuhe Pagoda (Pagoda of Six Harmonies) in Hangzhou, Zhejiang Province, is located on a turn of the Qiantang River near its outlet to the sea. When ships and boats come down the river during the daytime, sailors see the pagoda from a long distance and know they are approaching the turn near the river's mouth. At night it serves as an important mark to guide ships in the right direction. An ancient document says that "when ships wanted to anchor at night alongside the shore, they looked for beacon towers as guidance." Zishengsi Pagoda (Pagoda of the Holy Temple) at Haiyan, Zhejiang Province, served as a beacon tower. "Every storey of the pagoda was lit with square lamps; sailors on the East China Sea all looked for it as a guide in navigation." The pagoda at Jingtu Temple (Temple of the Pure Land) also "lit lamps all the night through for travelers to see as landmarks," as recorded in an ancient document. The purpose for building a pagoda at Futian Temple in Shanghai's Qingpu was simple and clear "as a beacon tower for travelers." Gusao Pagoda (Pagoda of Sisters-in-law) and Liusheng Pagoda (Pagoda of Six Victories) along the coast of Quanzhou Harbor in Fujian Province were both important navigation marks. Yingjiang Temple Pagoda at Anqing, Anhui Province, stood at a turn of the Yangtze River. It could be seen from a long distance during the daytime because it was such a tall building. At night several hundred lanterns on the pagoda illuminated the rolling waves of the river. A poem describing the scene reads, "Lighting up eight hundred lanterns on the pagoda, guiding a thousand ships on the river." Pagodas were also built near dangerous rapids and shoals in rivers and lakes, for in old times superstitious people believed pagodas could suppress the evils that might create dangers for travelers. Pagodas not only provided a sense of security, however, they also reminded people of the dangers at hand and helped them maintain vigilance.

Ancient pagodas marked ferry crossings and roads. In open country or wilderness a lofty pagoda could indicate the exact position of a bridge so that travelers did not have to go the long way round. A single pagoda or a pair of pagodas were sometimes built at a bridgehead, designed as an ornamental part of the bridge. Quite a few famous bridges built in old times, such as Luoyang Bridge at Quanzhou in Fujian Province, Anping Bridge at Jinjiang and Precious Belt Bridge at Suzhou in Jiangsu Province, were decorated with beautiful pagodas.

Researchers can consult the locations of ancient pagodas in their studies of geographic and topographic changes in history. For instance, at a place called Zhakou in Hangzhou stands a white stone pagoda believed to have been built between 907 and 960. Its present position is on top of a small hill in an environment of no particular significance, but eight to nine hundred years ago the Grand Canal ran into the Qiantang River at this spot. The pagoda is an important object of reference for study of the historic geography of the Hangzhou area.