Last year I almost drowned when I fell into an old well. The well was full of water because it had rained for two days.
I don't understand the problem you are having here.
'drowned' and 'fell' : past tense
'was' : past tense
then : the well was full of water at the time when he fell, because before that - two days previous to that - further back in time and the reason why the well was full : 'it had rained'
Perhaps you can post one of these long passages that are confusing you.