<p>This study examines the performance of an innovative electroecological system for treating brackish sewage in five cycles with different salinity concentrations. Two systems were designed: a control and electroecological system using a halophytic-constructed wetland (<i>Juncus rigidus</i>, retention time 96&#xa0;h) and an electrolytic cell (graphite electrode, external electric potential of 12&#xa0;V applied for 8&#xa0;h). The system effectively removed pollutants such as salinity (48–61.94%), COD (83.56–87.76%), BOD₅ (94.90–96.55%), TSS (90–92%), PO₄³⁻-P (98.46–99.6%), NH₄⁺-N (99.65%), NO₃⁻-N (71.94–91.96%), and NO₂⁻-N (79.66–86.88%) were achieved along with heavy metals like Cr (99.9%), Mn (47–55.97%), Mo (60.14–99.9%), Cd (30.77–99.9%), Zn (11.21–18.78%), and Al (14.93–99.9%) from wastewater and followed first-order kinetics. The electroecological system’s effectiveness was validated using statistical techniques like PCA and the Mann–Whitney <i>U</i> test. Pathogens, including <i>Vibrio</i>,<i> E. coli</i>,<i> Pseudomonas</i>, fecal <i>Coliform</i>, and <i>Aeromonas</i>, were nearly 99.9% removed, along with 99% of organic compounds, including emerging pollutants. Ion chromatography and inductively coupled plasma were used to study the accumulation of ions (Cl⁻, SO₄²⁻, Na⁺, K⁺, Mg²⁺, and Ca²⁺) in <i>Juncus</i> and their removal in water (around 83.15% K⁺, 30.53% SO₄²⁻, 29.53% Cl⁻, 26.45% Mg²⁺, 13.58% Na⁺, and 9.50% Ca²⁺). <i>Juncus</i> was efficient in accumulating K⁺ (66.99%) and Mg²⁺ (42.32%) ions. The electroecological system’s physical and biochemical analysis shows no salinity stress, showing potential for treating brackish sewage. No research has been reported on treating brackish sewage using a <i>Junucs</i>-based CW-electrolytic cell in the literature. It is a novel approach for independent wastewater treatment in coastal, remote, and rural areas.</p>