The addition of the variable sea level function to minecraft allows the set sea level of 64 to fluctuate during periods of extended specific weather conditions.
With the addition of variable sea level functionality, for every in-game day that the weather condition of rain, snow, or thunderstorm is present, the active sea level will increase by one block height. Increased sea level includes the ocean as well as individual lakes and ponds alike. Increased sea level covers all blocks that would have normally been uncovered at at sea level one block lower. Flooding can become a serious issue for access to buildings and farms built at sea level.
With fluctuating sea level, for every (1-x) days, (x being the percentage of time precipitation occurs, which I have not yet been able to find) the sea level will decrease by one block height. Lowering water levels can uncover underwater cave entrances and spots of clay. Man-made water sources (i.e. in farms, etc.) places at the current sea level will also go dry. For some farm-based food economies drought can become a serious issue, so it is suggested to build farms a good bit above the normal sea level.
In order to be safe from both effects of varying sea level, it is suggested to build man-made structures a good few blocks above sea level to avoid drought and flood effects. However, going as far as to only building on mountains and other extremes is unncessesary, as the law of averages dictates the sea level should in most circumstances never fluctuate more than a couple blocks at once.