Water quality measurements can indicate carbon status or algal biomass. Microalgae have an excellent ability to utilize all forms of dissolved inorganic carbon at different pH conditions. Water quality signature (WQS) using three different expressions with (i) pH; (ii) total alkalinity, hardness and total dissolved solids; and (iii) nitrate and conductivity of water was assessed in 32 wetlands distributed across 5 districts of West Bengal, India. Two zones were clearly discernible: coldwater (15–23 °C) high-altitude lakes in Darjeeling, and tropical (31–32 °C) low-altitude wetlands. Multivariate analysis of the Akaike information criterion (ACI) model revealed location-specific variability of agro-climatic and biogeochemical interactions. Dissolved inorganic carbon and inorganic nitrogen appeared to be important in regulating the phytocarbon content of microalgae. The wetlands located in the Gangetic alluvial tropical or semi-coastal areas (Hooghly, 24-Parganas, Nadia, Midnapore) were alkaline (pH = 7.52–7.97) where half-bound carbon dioxide comprised the major component (18–26%) of total inorganic carbon, with moderate to eutrophic (PO4-P− 0.16–0.23 mg/l) states which have a negative feedback to global warming. The heterogeneity of measured water quality signature consolidated the sanative nature of wetlands for their complex functional attributes with agro-climatic, biogeochemical and soil-water-biological interactions.