If you have demanding monitoring tasks see if you can get advice from your Environment Protection Authority on containers and preparation.
For most WaterWatch tasks it should be enough to use recycled soft drink bottles, about 500 ml capacity, which have been well washed and rinsed.
The PET soft drink bottles which I find littering our streets are light and very strong. Re-using these is comforting. Wash with hot water and detergent, and then triple rinse them carefully.
Sampling
When selecting a spot from which to sample first check for any flows coming in from side streams or drains.
It is best to sample well downstream of any confluence to ensure that mixing of the waters has been thorough, as the separate incoming streams may be measurably different in quality. Some rivers are famous for the distance down which the water from two different tributaries can be clearly distinguished.
If there are major differences in two converging streams consider monitoring each separately.
The choice may depend upon whether your major task is to provide an indication of the average quality of water moving downstream, or whether you are trying to monitor the effects of activities upstream.
Sampling should be done from about the middle of the stream, in the main flow, to minimise effects of mud or groundwater seepage from the banks. To do this you might have to make a long rod or pipe with a wire bottle holder on its end.
Timing
Reliable monitoring is regular, best done at the same time of day, as the chemistry of a watercourse varies depending upon sunlight and temperature.
Much of the significant activity of a stream occurs during 'events', such as rainstorms and floods. So it is important to get samples in conditions both of flood and drought.
Quality Control
Triple rinse your bottle using water from the sampling point, to ensure that the final sample is as representative of the stream as possible. Pour your rinse water out downstream or onto the bank.
Try to consider and eliminate any factors which could affect the quality of your results. I have to keep the dog on the leash until sampling is finished, as she cannot resist playing in the water.