The BioSand filter (BSF) is a household scaled, intermittently operated, slow sand filter. The BSF requires maintenance to remove trapped sediments. This study evaluated the effects of maintenance on the filter's flow rate and performance. Four concrete BSFs received three styles of maintenance: surface agitation (SA), stirring method (SM), and sand removal (SR). Effluent water was collected from the filter between 0–2 L effluent (0–2 L effluent) and between 15–20 L effluent (15 L+ effluent). After maintenance, effluent at 15 L+ (no pause time) showed a significant decrease in thermotolerant coliform removal rates by 0.66–0.91 log (SA), 0.57–0.67 log (SM) and 0.32–0.83 log (RM) (<0.001). Effluent water at 0–2 L (with pause time) did not significantly decrease in thermotolerant coliform removal rates (>0.17) for any maintenance method. The recovery duration after maintenance for all methods at 0–2 L effluent had a median recovery of <1.2 days. The effluent at 15 L+ had a longer recovery period (at least 3.9, 3.0 and 12.75 days for the SA, SM, and SR method, respectively). The flow rate recovery for SA (76%) and SM (82%) was lower compared to SR (138%).