The Magdalena River is the main fluvial artery of Colombia, communicating main urban centers of the country like Medellín and Bogota with the ports of Cartagena and Barranquilla in the Caribbean Sea. In recent years, Colombia has had a series of investments in port infrastructure on the Magdalena River, which join the initiative of the national government to revive the transportation of the most important waterway in Colombia. Gómez Cajiao, a leading company in Colombia in port infrastructure design, presents the current challenges and the solutions implemented in the design of ports from the hydrological and hydraulic point of view and the impact that climate change has had on port infrastructure designs. Experiences and challenges in the understanding the effect of climate change on the design of port infrastructure are presented; the impact on the environment from an Eco-hydrological point of view and the social effects considered in the design of the hydraulic solutions of the projects that are presented as case studies. The port projects on the Magdalena River present environmental challenges related to water management in wetlands, which are habitat of several species and support for families of fishermen who develop their productive activity there. The effect of climate change is analyzed as an increase in extreme flows and the possible effects of planned works in the river basin and affecting the flow regime, such as hydroelectric and reservoirs, are discussed.