The concerns of dye in an aquatic system associated with acute toxicity and carcinogenicity, and the increase in demand for hydrogen production has led to a keen interest in advancing solar driven methodologies utilizing potent photocatalysts to address environmental concerns through sustainable remediation practices. In this pursuit, we synthesized a heterostructure comprised of Fe doped MoO3 (Fe:MoO3), anchored on g-C3N4 sheet as a photocatalyst denoted as Fe:MoO3/g-C3N4, employing a sonication supported green synthesis method with the aid of Murraya paniculata leaf extract. We explored structural, morphological, and surface characteristics using various analytical techniques, including X-Ray diffraction (XRD), Fourier transform infrared (FTIR) spectroscopy, UV–visible spectroscopy, Field emission scanning electron microscopy (FE-SEM) and High-resolution transmission electron microscopy (HR-TEM), X-Ray photoelectron spectroscopy, and BET for a comprehensive surface analysis. The outcomes highlighted the exquisitely oriented and interconnected arrangement of MoO3 nano rods ensconced within a piled layer of g-C3N4. The XRD patterns unveiled the coexistence of g-C3N4 and Fe:MoO3 within the heterojunction structure. FESEM and HRTEM image analysis of Fe:MoO3/g-C3N4 heterojunction reveals a g-C3N4 nanosheet wrapping the Fe:MoO3 nanoparticles with the formation of nanorods of MoO3 with an average thickness of 9.46 nm containing circular Fe nanoparticles with a mean diameter of 8.97 nm. This intricate configuration resulting in a decrease of the size of the nanoparticle caused by effective sonication-supported green modulation configuration facilitated an optimized charge flow, contributing to the elevated photo assisted catalytic performance of the heterojunction. The Fe:MoO3/g-C3N4 semiconductor heterojunction exhibited a considerable surface area and pore volume, inherently amplifying the sites of the activity on the surface and thereby enhancing photoactivity. As opposed to both g-C3N4 and the Fe:MoO3 nanoparticles, the Fe:MoO3/g-C3N4 semiconductor heterojunction showcased enhanced photocatalytic effectiveness in the degradation of dye Crystal violet (CV). Under optimized circumstances, the photo assisted degradation of dye CV by the semiconductor heterojunction adhered to pseudo-first-order kinetics. The active species responsible for the photo assisted degradation process is identified as •O2−. These findings not only emphasize the enhanced efficacy of the developed semiconductor heterojunction but also reveal its potential for addressing the environmental challenges posed by dye CV contamination through prolonged and efficient photocatalytic remediation practices. A marked improvement in both photo assisted catalytic and photoelectrochemical (PEC) water splitting activities under visible light exposure was showcased. The augmented performance of the Fe:MoO3/g-C3N4 semiconductor heterojunction in photodegradation and PEC water splitting activities can be attributed to the extended absorption of visible light. Additionally, the synergistic influence of g-C3N4, contributes positively to the separation of charges and expedites the transfer efficiency of photogenerated charge carriers. This synergy enhances the overall effectiveness of the nanoparticles in harnessing visible light for efficient water-related processes.