The study examined the security challenges along the commercial water routes of Bayelsa State, Nigeria. A total of 320 copies of a questionnaire on the operators and passengers in the study area to elicit information from the operators and passengers in the eight selected Bayelsa waterfronts. Both descriptive and inferential statistics were used for the data analysis. Findings showed that the Nembe-Brass route, Oporoma-Yenagoa route, Yenagoa-Brass route and Ogbia-Brass route are commercially viable routes making them enticing routes both for transportation and pirates and robbers attacks. Furthermore, Also, piracy/sea robbery, cultism, smuggling, kidnapping and illegal oil bunkering were identified as the major types of security challenges that are common in the Bayelsa waterways. However, evening and night periods experience more attacks than all other periods of the day. Unemployment, underdevelopment, illiteracy, lack of adequate security and poverty, cost and availability of fuel, lack of navigation aid, decrease in water level, multi-designated Nembe-Brass route, Oporoma-Yenagoa route, Yenagoa-Brass route and Ogbia-Brass route are commercially viable routes making them enticing routes both for transportation and pirates and robbers attacks authorities were the main causes of insecurity on Bayelsa waterways. It is recommended among others that the commercial water transport routes in Bayelsa State should be constantly dredged intermittently by State government to enable bigger ships to ply the routes thereby enabling more commercial activities; both Federal, State, Local governments and Inland waterways transport regulatory bodies should make available navigational aid and adequate security along the routes to avert any variety of security challenges.