A pot experiment was conducted to investigate the effect of industrial effluents on the morphological and anatomical structures of Capsicum annuum var Cayenne. The treatments comprised 0% (control), 5%, 10%, 15% and 20% industrial effluent concentrations, applied as irrigation water. The effluent and soils irrigated with the effluent concentrations were analysed for various parameters including pH, temperature, conductivity and heavy metals. Growth data were collected fortnightly until the eighteenth week when the experiment was terminated. The results revealed an increase in the heavy metal toxicity in the soils with increase in the effluent concentrations. There was significant reduction (P < 0.05) in the plant height, stem girth, leaf length, leaf diameter, number of flowers, number of fruit, fruit weight, plant weight and root length with increased effluent concentrations. The significant reduction in the growth parameters was more pronounced on plants irrigated with 15% and 20% effluent concentrations. The morphological response of the plants to the various effluent concentrations contributed to the reduction in the anatomical characters studied. Stem tissues such as cortical layer, vessel number, pith thickness, collenchyma and parenchyma cell thickness decreased significantly with increased effluent concentrations. The highest mean cortical layer thickness (12.38 mm), pith thickness (41.00 mm) and parenchyma cell thickness (6.25 mm) was observed in C. annuum with no effluent (0% concentration) while the lowest mean cortical layer thickness (5.63 mm), pith thickness (32.88 mm) and parenchyma cell thickness (3.25 mm) was observed in C. annuum irrigated with 20% effluent concentration. The root and petiole tissues also showed similar trends. The application of higher concentrations of the effluent contributed to increase in the heavy metal toxicity in the soils, thereby, resulting in the reduction in the growth of the Capsicum annuum as well as the anatomical structures.