To assist reaching net-zero emissions, the dissolved carbon in the ocean can be extracted to enable an indirect air capture. An electrochemical bipolar membrane electrodialysis (BPMED) is a sustainable method for such capture. The BPMED enables a pH-swing that manipulates the oceanic carbonate-equilibrium using electricity. However, at alkaline-pH, an in-situ process suffers from inorganic fouling within the stack, increasing the cost of capture. In the current work, we investigate fouling management strategies including fouling control (i.e., membrane- configuration and current-flow rate optimization) and fouling removal methods. Fouling removal methods including air and CO₂(g) sparging, dissolved CO₂ (aq) cleaning, back-pressure, flow rate increase, and acid-wash are investigated under accelerated fouling conditions. The stack configuration containing the BPM-AEM pairs shows 4 × lower fouling than the BPM-CEM stack, while the carbonate-extraction and faradaic efficiency are similar for both configurations. From the scaling removal methods, only the acid wash combined with the back-pressure removed all the inorganic fouling, recovering both the cell voltage and pressure drop to their initial values. Upon the air sparging, the total cell voltage and pressure drop increased even more due to the trapped gas inside the netted spacers. Cleaning via dissolved and gaseous CO₂ decreases the cell pH, dissolving hydroxide/carbonate-based fouling, but decreases the carbonate-removal significantly which is not preferred. Applying the back-pressure and higher flow rates decelerated the scaling buildup but was not enough to remove the fouling. Using BPM-AEM stacks in combination with periodic acid cleaning has potential as resilient oceanic carbon removal via BPMED.