The potential negative influence of the seaweed Caulerpa prolifera on the seagrass Cymodocea nodosa was explored in a Mediterranean coastal lagoon (Mar Menor, Spain) where the alga suddenly and rapidly spread four decades ago. An extensive field sampling was carried out across the lagoon to characterise the distribution and abundance of both macrophytes at different spatial scales, as well as sediment characteristics. Generalised linear and additive models were performed at the whole-lagoon scale, for deep and shallow bottoms, independently, to explore factors influencing C. nodosa distribution and abundance. A high-spatial-resolution macrophyte distribution map was also generated by integrating underwater imaging, direct visualisations and orthophotographs. This map showed that both macrophytes largely dominated the ecosystem but with opposing depth patterns of abundance that mainly reflected their specific light requirements. C. nodosa was dominant at shallow depths but also grew intermingled with a dense C. prolifera bed over large areas of the deep seafloor with highly anoxic muddy sediments. Models did not reveal overall negative relationships between the macrophytes, indicating that C. prolifera was not the main driver of C. nodosa distribution and abundance in this coastal lagoon. Findings highlighted the absence of a negative direct or indirect influence of C. prolifera on C. nodosa, as supported by the fact that the distributions of both macrophytes were similar to those reported in the 1980s, just a few years after C. prolifera had spread in the lagoon. We conclude, therefore, that C. prolifera is not progressively replacing C. nodosa in this ecosystem, where both species have coexisted for decades.