A filter system for filtering water and/or wastewater that includes a roughing filter followed by a polishing filter where the roughing filter is an upflow filter and the polishing filter is a membrane filter. The upflow filter includes a filter bed formed from one or more layers of media. The media may be naturally occurring or plastic. Further, the media may be buoyant or non-buoyant. Preferably, the filter system is formed as a package unit. The upflow filter and membrane filter may share a common base allowing the filter system to be readily transported as a single unit. Alternatively, the membrane filter may be connected to and supported by a vertical wall of the upflow filter. The membrane filter may include membrane filter modules that are housed as a group in a section of the membrane filter or the membrane filter modules may be individually housed. The washing liquid used in washing the upflow filter may be discharged from the upflow filter through the same conduit as the upflow effluent generated during filtration. Preferably, the upflow waste line is positioned adjacent the membrane filter drain to allow the upflow waste line and the membrane filter drain to direct liquid to the same storage area or unit through at least one common conduit. The water level of the clearwell is preferably positioned a sufficient distance below the water level of the upflow filter to achieve the desired loading rate across the membrane filter without the need for pumping the upflow effluent into the membrane filter.