Microplastics are emerging pollutants that have been found in different environmental matrices of marine and coastal ecosystems, where they can generate harmful ecological impacts. Little is known about the current state of microplastic pollution in fragile tropical lagoon ecosystems, such as Ciénaga Grande de Santa Marta (CGSM) in the Caribbean coast of Colombia. This study assesses microplastic pollution in surface waters and sediments, and the occurrence of microplastic ingestion in commercially important fish species from CGSM. In waters, microplastic abundances ranged from 0.0 to 0.3 items L−1 while in sediments they varied from 0.0 to 3.1 items kg−1. The most abundant types of microplastics are fibers and fragments, with polypropylene, polyethylene and high-density polyethylene as the most abundant polymers. Also, 100 (i.e. 21.1%) out of 474 individuals from nine fish species had microplastics in their digestive tracts. Microplastics present in water and sediments and in the digestive tract of the analyzed fish species have similar characteristics, also showing a moderate and statistically significant association. Microplastic abundances are higher near river mouths and in urban areas with a high density of fishing activities and aquaculture infrastructures, which are important sources of contaminants. Microplastic pollution in CGSM represents a threat to the lagoon ecosystem and to local people depending on artisanal fishing. Consequently, effective actions to reduce pollution and its socio-environmental impacts are urgently required.