Filtration systems having a normal filtration mode and an enhanced filtration mode are described. In some arrangements, the filtration system is an air filtration system having a primary air filter element, a pre-cleaner, and a pre-cleaner bypass valve. Based on feedback from an intake air quality sensor the bypass valve is either opened or closed to selectively route intake air through the pre-cleaner during sensed dirty air operating conditions (e.g., heavy dust or moisture concentrations). In other arrangements, the filtration system is a liquid filtration system (e.g., a fuel or oil filtration system) that has a main filter and a secondary filter. The filtration system selectively routes the liquid being filtered through the main filter, the secondary filter, or a combination thereof depending on a detected event or sensed characteristic of the liquid.