Your results will only be as coherent and comprehensible as your initial conception of the problem. Clearly define the statistical population to sample. Define the statistical population precisely on a local scale, draw statistical conclusions about it, then extrapolate to general conclusions about biological population. Define your sampling unit.
More dynamic systems require more frequent samples.
Take replicate samples within each combination of time, location, and any other controlled variable. Take an equal number of replicate samples for each combination of controlled variables. Calulate sample size based on power analysis. To test whether a condition has an effect, collect samples both where the condition is present and where the condition is absent but where all else is the same. An effect can only be demonstrated by comparison to a control.