In terms of ISO 17025; Sampling (clause 7.3), Handling of Samples (clause 7.4) and Facilities and environmental conditions (clause 6.3) conditions must be met. Record keeping, including chain of custody records are crucial. The actual best practices will depend on the parameter to be tested, and your sector / regulations. All will, however, cover sampling, preservation, handling, transport and storage. The requirements for microbiological, chemical, toxicological and biological assays differ widely, and cannot unfortunately be detailed in this response. There are International and National standards available, as well as guidance from organisations such as WHO, EPA and FDA; that you can look at.
Have a look at the ISO International Classification for Standards (ICS) 13, for Environment, Health protection and Safety (https://www.iso.org/ics/13/x/) with 13.060 covering Water Quality (https://www.iso.org/ics/13.060/x/). Here, for example, you will find access to ISO 5667-3:2018 Water quality — Sampling — Part 3: Preservation and handling of water samples. For microbiology look at ISO 19458:2006 Water quality — Sampling for microbiological analysis.