Replace as needed. Filter water from top of the container. For an added precaution, separate your intake hose from your output hose. Minimizing cross-contamination helps reduce the risk of ingesting microbiological contamination. Use a reclosable food bag to keep your hoses separate, and to keep your pack dry.
Surface water is one of many sources for becoming sick from microbiological contamination.
Unfortunately there are many avenues for contamination. For these reasons, it is important to maintain proper sanitary conditions in the back country. A water treatment system is only one part of the equation. Make sure the black or red shipping caps are removed from your filtration unit before the intake and product water hoses are installed. Yes, even experienced users have made this mistake.