The process of water sampling introduces two significant problems:
* The first problem is the extent to which the sample may be representative of the water source of interest. Water sources vary with time and with location. The measurement of interest may vary seasonally or from day to night or in response to some activity of man or natural populations of aquatic plants and animals. The measurement of interest may vary with distances from the water boundary with overlying atmosphere and underlying or confining soil. The sampler must determine if a single time and location meets the needs of the investigation, or if the water use of interest can be satisfactorily assessed by averaged values of sampling over time and location, or if critical maxima and minima require individual measurements over a range of times, locations or events. The sample collection procedure must assure correct weighting of individual sampling times and locations where averaging is appropriate. Where critical maximum or minimum values exist, statistical methods must be applied to observed variation to determine an adequate number of samples to assess the probability of exceeding those critical values.
* The second problem occurs as the sample is removed from the water source and begins to establish chemical equilibrium with its new surroundings – the sample container. Sample containers must be made of materials with minimal reactivity with substances to be measured; pre-cleaning of sample containers is important. The water sample may dissolve part of the sample container and any residue on that container, and chemicals dissolved in the water sample may sorb onto the sample container and remain there when the water is poured out for analysis. Similar physical and chemical interactions may take place with any pumps, piping, or intermediate devices used to transfer the water sample into the sample container. Water collected from depths below the surface will normally be held at the reduced pressure of the atmosphere; so gas dissolved in the water will collect at the top of the container. Atmospheric gas above the water may also dissolve into the water sample. Other chemical reaction equilibria may change if the water sample changes temperature. Finely divided solid particles formerly suspended by water turbulence may settle to the bottom of the sample container, or a solid phase may form from biological growth or chemical precipitation. Microorganisms within the water sample may biochemically alter concentrations of oxygen, carbon dioxide, and organic compounds. Changing carbon dioxide concentrations may alter pH and change solubility of chemicals of interest. These problems are of special concern during measurement of chemicals assumed to be significant at very low concentrations.
Sample preservation may partially resolve the second problem. A common procedure is keeping samples cold to slow the rate of chemical reactions and phase change, and analyzing the sample as soon as possible; but this merely minimizes the changes rather than preventing them. A useful procedure for determining influence of sample containers during delay between sample collection and analysis involves preparation for two artificial samples in advance of the sampling event. One sample container is filled with water known from previous analysis to contain no detectable amount of the chemical of interest. This sample, called a "blank", is opened for exposure to the atmosphere when the sample of interest is collected, then resealed and transported to the laboratory with the sample for analysis to determine if sample collection or holding procedures introduced any measurable amount of the chemical of interest.  The second artificial sample is collected with the sample of interest, but then "spiked" with a measured additional amount of the chemical of interest at the time of collection. The blank (negative control)  and spiked sample (positive control) are carried with the sample of interest and analyzed by the same methods at the same times to determine any changes indicating gains or losses during the elapsed time between collection and analysis.