Obviously it's better if you have base line data . Is your site typical , how much variation is there, how many more sites will you need, select a control , a nearby site. Make sure you sample in all weathers , especially if there is a sudden change a snow melt, a huge flood, or a hot spell or a known or suspected pollution incident. Low flows may give atypical results, high flows may be very difficult to sample and give a false reading. Are you going to sample qualitatively or quantitatively .
Different rules apply.
Qualitative methods need you to make sure you look at every habitat type but the number of samples is unimportant. There comes a time when the number of extra species obtained from each repeated sample drops off, and this is the point when in theory you should stop sampling. Quantitative sampling need good statistical analysis techniques, number of duplicates etc. But if you sample too much as a small site you can damage it. Some animals are found in clumped distribution therefore their results difficult to interpret, e.g. Blackfly larvae.