We studied the relative value of natural habitats, river and coastal wetlands, and artificial habitats, irrigation canal and ponds, for the conservation of an endangered fish, Iberian toothcarp, in its southernmost area of distribution, characterised by agricultural intensification. Our results show that the bulk of the population of the Iberian toothcarp is concentrated in irrigation ponds. Natural habitats sustained null or impoverished subpopulations, and individuals showed signs of low metabolic activity. This coincided with the relatively high habitat quality observed in ponds, particularly those with submerged aquatic vegetation, in contrast with the chronic eutrophication of the coastal lagoons. In spite of a generalised aggressive management in the irrigation system, featured by periodic vegetation clearance, desiccation and biocide treatment, the subpopulation of the Iberian toothcarp thrives in it probably thanks to adequate water quality and to an active path dynamics maintained by connectivity through the canal. Agro-environmental measures are discussed for the improvement of this species conservation in natural and artificial habitats.