One of the main challenges for the implementation of electrocoagulation (EC) in water treatment are fouling and passivation of the electrodes, especially for applications with high contaminant concentrations. For the first time, we investigated in this study the process of fouling mitigation by polarity reversal during the EC treatment of boiler blowdown water from oil-sands produced water, characterized by high silica concentrations (0.5–4 g L−1). This effluent is typically obtained from an evaporative desalination process in oil production industries. Potentiodynamic characterisation was used to study the impact of passivation on the anode dissolution. Although a charge loading of 4,800 C L−1 was found to remove about 98% of silica from a 1 L batch of 4 g L−1 Si solution, fouling reduced the performance significantly to about 40% in consecutive cycles of direct current EC (DC-EC) treatment. Periodic polarity reversal (PR) was found to reduce the amount of electrode fouling. Decreasing the polarity period from 60 to 10 s led to the formation of a soft powdery fouling layer that was easily removed from the electrodes. In contrast, with DC operation, a hard scale deposit was observed. The presence of organics in the field samples did not significantly affect the Si removal, and organics with high levels of oxygen and sulfate groups were preferentially removed. Detailed electrochemical and economic investigations suggest that the process operating at 85 °C achieves 95% silica removal (from an initial concentration of 481 mg L−1) with an electrical energy requirement of 0.52 kWh m−3, based on a charge loading of 1,200 C L−1, an inter-electrode gap of 1.8 cm and a current density of 16 mA cm−2.