This study investigated the effects of nutrient concentrations (0, 0.8, 1.6, 2.4, and 3.2 dS m⁻¹) and substrate types (volcanic sand, rice husk charcoal, and a 1:1 mixture) on Limnocharis flava growth and rhizosphere bacterial morphological diversity in a hydroponic system. A factorial experiment was arranged in a randomized complete block design (RCBD) with three replications. Low to moderate nutrient levels (0.8–1.6 dS·m⁻¹) enhanced the leaf area ratio (LAR), relative growth rate (RGR), net assimilation rate (NAR), and harvest index (HI), while rice husk charcoal and the mixed substrate supported greater plant growth and root volume. Bacterial density increased under low nutrient concentrations but declined at higher levels. A total of 138 bacterial isolates were obtained and classified into 23 morphotypes based on macroscopic traits. Diversity analysis showed Shannon–Wiener and Simpson index values ranging from 0.2–1.6 and 0.2–0.75, respectively, indicating low to moderate diversity. Higher diversity was associated with nutrient concentrations of 0–1.6 dS·m⁻¹, whereas elevated levels promoted dominance. Substrate type did not significantly affect bacterial density or pH but strongly influenced root volume, with volcanic sand and mixed substrates providing better aeration and porosity. These findings demonstrate that nutrient substrate interactions regulate both plant morpho-physiological traits and rhizosphere bacterial structure, offering a basis for sustainable hydroponics and potential biofertilizer applications.