Water quality index (WQI) models are generally used in hydrochemical studies to simplify complex data into single values to reflect the overall quality. In this study, deep groundwater quality in the Chittur and Palakkad Taluks of the Bharathapuzha river basin of Kerala, India, was assessed by employing the WQI method developed by the Canadian Council of Ministers of the Environment (CCME). The assessment of overall water quality is indispensable due to the specific characteristics of the study area, such as geography, climate, over‐drafting, and prevalent agricultural practices. Forty representative samples were collected from the study area for monsoon (MON) and pre‐monsoon (PRM) seasons. The results showed a general increase of contents from MON to PRM. The major cations were spread in the order Ca2+>Na+>Mg2+>K+ and the anions HCO3−>Cl−>CO32− based on their relative abundance. Among various parameters analysed, alkalinity and bicarbonate levels during MON were comparatively high, which is indicative of carbonate weathering, and 90% of the samples failed to meet the World Health Organization (WHO, 2017)/Bureau of Indian Standards (BIS, 2012) drinking water guidelines. The CCME WQI analysis revealed that nearly 50% of the samples during each season represented good and excellent categories. The samples in the poor category comprised 10% in MON and 15% in PRM. The overall WQI exhibited 15% of poor category samples as well. The spatial depiction of CCME WQI classes helped to expose zones of degraded quality in the centre to eastward parts. The spatial and temporal variations of CCME WQI classes and different physicochemical attributes indicated the influence of common factors attributing to the deep groundwater quality. The study also revealed inland salinity at Kolluparamba and Peruvamba stations, where agricultural activities were rampant with poor surface water irrigation.