I dont understand why (if you think the variation in temperature is between months) you are measuring multiple times in one month to address this. It would seem the way to address this would be to measure in different months and control for this. I may misunderstand your point or method
You want to measure what you are controlling for or think the key variables are. I would think if month is a key variable and spartial variation then you need samples that allow you to compare by month and by spartial variation. For example if soil ph and temperature were both issues you would want to have say an acid and non acid sample in month x and the same in month x+2.
On the other hand I had a single graduate DOE course so that might be simplistic.