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Context: Preserving hydrophyte and wetland plant diversity is among the most critical environmental issues worldwide. The progressive decline and disappearance of these species led to dramatic consequences on functions and services provided by inland aquatic ecosystems. This is especially relevant for lowlands that are usually disturbance-dominated landscapes, mainly by mechanization in agriculture and land use changes. Objectives: In these contexts, it is fundamental to understand the key factors affecting the aquatic and wetland plant richness, focusing on relict aquatic habitats, and overcoming a purely trophic-oriented approach. Methods: To do this, the aquatic and wetland flora of 88 aquatic sites, encompassed in an oversimplified watershed, was explored in terms of the total number of aquatic and wetland plant species, hydrophytes, alien species, and policy species, as well as 18 explanatory variables, including eco-morphological, hydrological, direct human impact, and landscape mosaic drivers. Results: The results emphasize the key role of site area and hydrological connectivity compared to land-use intensity in explaining hydrophyte and wetland plant richness in overexploited landscapes; conversely, site origin was crucial only for alien species, being more abundant in artificial sites. Conclusions: This paper offers a new comprehension of the leading contribution of local drivers in explaining macrophyte patterns, suggesting a relevant influence of habitat dynamics in regulating species establishment and developing. The future challenge will be to actively include artificial and/or altered aquatic ecosystems in hydrophyte and wetland plants conservation programs, not forgetting the risks associated with an increasingly spread of alien species. Graphic Abstract: [Figure not available: see fulltext.].