Potholes are microhabitats in riverine ecosystems, which contribute substantially to the unique regional faunal diversity and community composition. The potholes of riverine habitats of Kerala are less explored, thus this study is of signi cant importance for riverine health assessment using entomological indicators. A total of 18 potholes were identi ed from the two stations located in the Chalakudy river basin according to their vertical pro le. Insects were sampled monthly along with water quality parameters. We could identify 208 individuals represented by 15 families in the Athirappilly (S1). Among the collected taxa Ephemeroptera was the dominant order comprised of 48.56% of the population. Only 94 individuals represented by 10 families reported from the Ezhattumugham (S2). Hemiptera was the dominant order and comprised 51.06% of the total taxa collected. Benthic metrics such as family biotic index (FBI), % of Ephemeroptera Plecoptera, Trichoptera taxa (EPT), % of Ephemeroptera taxa, and % of tolerant organisms indicated remarkable variation in water quality status among the two stations and there was a signi cant difference in benthic metrics (p < 0.05). Major functional feeding groups reported, the percentage contribution of predators (p = 0.010), shredders (p = 0.009), and scrappers (p = 0.007) exhibited statistically signi cant variations between stations. Insects belonging to the families of Baetidae, Ephemeridae, Perlidae, and Stenopsychidae were found to be the most sensitive forms reported from the S1 indicates good water quality condition. Contrastingly, insects belonging to the families of Micronectidae, and Chironomidae being pollution-tolerant taxa, were abundant at S2 indicates a fairly poor condition of the potholes.