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The aim of this study was to provide technical means and data support for enhancing the filtration pretreatment capacity of the recirculating aquaculture system. A continuous flow electrocoagulation (EC)-filtration system was designed and its application in the pretreatment of marine aquaculture wastewater was studied. The influences of anode combination modes, hydraulic retention times (HRTs) of the EC reactor and filter pore sizes on the water treatment capacity were investigated. Results showed that EC could significantly enhance the treatment efficiency of the filtration equipment used in subsequent steps. Al-Fe electrodes used as anode led to better processing capacity of this system, and the optimum anode was 3Al + Fe. With the increase of HRT and decrease of filter pore size, the enhanced effect of the EC process on filter was more obvious. When the current density was 19.22 A/m2, the anode was 3Al + Fe, the HRT was 4.5 min and the filter pore size was 45 μm, the removal efficiency of system for the total number of vibrio, chemical oxygen demand (CODMn), total ammonia nitrogen (TAN), nitrite nitrogen (NO2−-N), nitrate nitrogen (NO3−-N) and total nitrogen (TN) was 69.55 ± 0.93%, 48.99 ± 1.42%, 57.06 ± 1.28%, 34.09 ± 2.27%, 18.47 ± 1.88%, 55.26 ± 1.42%, respectively and the energy consumption was (26.25 ± 4.95) × 10−3kWh/m3.