Coastal wetlands are ecosystems that provide multiple benefits to human settlements; nonetheless, they are seriously threatened due to both a lack of planning instruments and human activities associated mainly with urban growth. An understanding of their functioning and status is crucial for their protection and conservation. Two wetlands with different degrees of urbanization, Rocuant-Andalién (highly urbanized) and Tubul-Raqui (with little urbanization), were analyzed using temperature, salinity, dissolved oxygen, pH, turbidity, granulometry, fecal coliform, and macroinvertebrate assemblage variables in summer and winter. In both wetlands marked seasonality in salinity, temperature and sediment texture classification, regulated by oceanic influence and changes in the freshwater budget, was observed. In the Rocuant-Andalién wetland, the increases in pH, dissolved oxygen, gravel percentage, and coliform concentration were statistically significant. Urbanization generated negative impacts on macroinvertebrate assemblage structure that inhabit the wetlands; greater richness and abundance (8.5 times greater) were recorded in the Tubul-Raqui wetland than in the more urbanized wetland. The multivariate statistical analysis reflects the alteration of these complex systems.