An assessment of the pollution status of Museum Lake in the Thiruvananthapuram Botanical Garden and Museum was conducted. Analysis of different community structures of the planktonic taxa in the lake revealed it is organically polluted, attributable to the organic litter from riparian vegetation. A total of 30 most pollution‐tolerant phytoplankton genera and 24 pollution‐tolerant species were identified. Pollution‐tolerant phytoplankton genera in the lake included Chlorophyceae, Bacillariophyceae, Cyanophyceae and Euglenophyceae. Scenedesmus, Pinnularia, Euglena, Ankistrodesmus, Closterium, Crucigenia, Kirchneriella, Merismopedia and Oscillatoria were some of the phytoplankton pollution tolerant genera whereas, Nitzschia palea, Synedra acus, Scenedesmus quadricauda, Pandorina morum and Trachelomonas volvocina were some of the pollution tolerant species noted. Excessive nutrient loading from the surrounding area is definitely degrading the quality of this urban lake ecosystem. Detailed information regarding the pollution status of a waterbody is very important in this regard, noting it ultimately assists in undertaking proper management of a waterbody. The Palmer Algal Index score for Museum Lake was 37, indicating it is highly organic enriched. The results of different algal indices (e.g. Chlorophycean Index; Nygaard Index) indicated a eutrophic condition for Museum Lake, being attributed to its increased organic enrichment. Canonical correspondence analysis between environmental variables and the microalgal bioindicators also highlighted the influence of the physical and chemical parameters on phytoplankton abundance and distribution in Museum Lake.

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