One of the first things to get your head around in controlled environment growing is that water is almost never clean. Even tap water, which has often been subject to sterilisation and treatment, will introduce some bugs into your system. As such, active management to limit the build-up or impact of this effect is highly important.
Water management can be achieved mechanically, chemically, or through approaches such as UV sterilisation. The best approach will depend on system and/or crop type, but some system for management will be necessary for almost all hydroponic systems (particularly ones that aim to ‘recycle’ water and nutrients in a recirculating system).