Membrane distillation (MD) is an emerging process with a proven ability to recover freshwater from streams with a wide range of salinities. However, MD is susceptible to biofouling. This study explores the efficiency of different cleaning strategies in biofilm removal during seawater MD. Hydraulic cleaning and chemical cleanings with 0.3%w w−1 ethylenediaminetetraacetic acid (EDTA), 0.3%w w−1 NaOCl, and 3%w w−1 citric acid were tested. The results showed that permeate flux recovery increased in the order of hydraulic cleaning <3%w w−1 citric acid <0.3%w w−1 NaOCl ≈0.3%w w−1 EDTA. Membrane cleanings substantially reduced the thickness of the residual biofilm layer and decreased its bacterial concentration and resistance to vapor pressure. The post-cleaning permeate conductivities were low suggesting that employed cleaning protocols did not cause pore wetting of hydrophobic polytetrafluoroethylene microporous (0.22 μm) membrane, and membrane rejection properties remained stable.