Full-scale application of membrane distillation (MD) requires effective pretreatment strategies to control biofilms, a persistent challenge of desalination systems. This study explores the impact of “shock” chlorination on the direct contact MD (DCMD) using Red Sea water under conditions similar to reverse osmosis plants. The DCMD performance at different feedwater temperatures was evaluated, and biofilm architecture and composition were linked to key performance indicators. Our results demonstrated that “shock” chlorination delayed microbial growth and reduced biofilm coverage and thickness. Another positive aspect is reduced scaling propensity by limiting salt entrapment and deposition of Ca and Mg salts on the membrane surface. As a result, improved permeate fluxes were achieved at 45 °C and 55 °C without compromising permeate quality. However, at 65 °C, induced pore wetting occurred due to combined thermal and oxidation effects that impaired membrane’s selectivity indicating that while “shock” chlorination controls biofilms at lower and moderate temperatures, its effectiveness diminishes with temperature increase. Our study highlights that proactive strategies, such as controlled “shock” chlorination, are essential for efficient MD performance. A practical approach is to implement this strategy for biofilm management under carefully optimized operating conditions to minimize fouling risks and support resilient seawater MD systems.