The overdependence on chemical fertilizers in conventional agriculture has led to severe ecological degradation, soil fertility loss and health concerns, prompting the urgent need for sustainable alternatives. This study investigates the biofertilizer potential of two aquatic macrophytes Azolla microphylla Kaulf. and Lemna minor L. on the growth, physiology and yield of Solanum lycopersicum L., under field conditions using Randomized Block Design (RBD). For these six treatments were tested such as control, Azolla, Lemna, combination of Azolla & Lemna, cow dung and NPK fertilizer, with three replications each. The growth parameters like plant height, number of branches, number of leaves, leaf area index and reproductive parameters like flowers and fruit count along with physiological parameters, chlorophyll (a, b, total) and carotenoid content were systematically recorded. The combined application of Azolla and Lemna significantly enhanced all measured parameters compared to both the control and NPK treated plots except for carotenoid content which show high value in Lemna only treatment than control and NPK plots. Notably 120.61% increase in plant height, 6463.63% increase in flower production and over 11-fold increase in fruit yield compared to control. Analysis of Variance (ANOVA) confirmed the statistical relevance (p < 0.001) of these effects. Physiological parameters such as chlorophyll a, b, total chlorophyll and carotenoids also showed significant enhancement. This study is novel in demonstrating the synergistic effect of Azolla and Lemna as biofertilizers, surpassing individual and chemical treatments. The dual application offers a low-cost, eco-friendly alternative that enhances crop yield, supports soil health, and promotes sustainable agriculture.