Phytoplankton, macrophytes and environmental parameters were used to determine the trophic status of Lakes Cazaux and Parentis with a four seasons sampling plan. Both natural lakes are located along the French Atlantic coastline and although a channel connects them, they have different trophic status. Lake Cazaux has almost conserved its pristine conditions despite the agricultural activities that have developed in the neighbourhood. This is confirmed by the few changes in the phosphorus and chlorophyll a concentrations, as well as in the phytoplankton composition (Stichogloea olivacea, Willea irregularis) observed in the last 30 years. Lake Parentis has been degraded for years by an active charcoal industry and petroleum exploitation. High phosphorus and chlorophyll a concentrations, little transparency and phytoplankton composition represented by Woronichinia naegeliana, Pediastrum boryanum and Microcystis aeruginosa characterise this lake. Macrophytes are represented in both lakes by Phragmites australis and Scirpus pungens, however, in Lake Cazaux the protected Lobelia dortmanna is predominant while it was not observed in the studied area of Lake Parentis. Our results confirm the mesotrophic and eutrophic status of Lakes Cazaux and Parentis respectively, and could contribute with the ecological status assessment recommended for the Water Framework Directive.