Water reuse for agricultural irrigation can contribute to the conservation of valuable water resources and opens the possibility to reuse the wastewater's nutrients (N and P) at the same time. As irrigation is usually limited to vegetation periods, effluent requirements for treated wastewater may vary seasonally. A process concept for wastewater treatment with variable operation modes for the seasonal production of nutrient-rich irrigation water and nutrient-poor discharge water is proposed. It is shown that a two-step process consisting of organics removal followed by biological aerated filters (biofilters) for nitrogen removal is a promising combination which allows a flexible and seasonally varied operation with a fast re-start of biological nitrification after shut-down periods. To date, there is no commonly accepted practice amongst operators to take biofilters out of service for periods of time while - at the same time - maintaining biological activity to enable a quick start-up. This paper shows that during shut-down periods the activity drop rate is the smallest if the filter bed is maintained flooded and without aeration; then a very quick re-start is possible.