Whenever it seems like two water levels should be equal but aren't, either there is a physical restriction preventing flow (like a dam keeping upstream waters higher than downstream, or surface tension causing meniscuses or capillary action), or there is energy being expended to put water back upstream as fast as gravity is pulling water downstream.
In a sump, the lower water level can be maintained despite water continously flowing into it is due to there being a pump at the bottom, consuming electrical energy to move water from that lower section back to the higher section. So there appears to be continuous flow of water yet no change in the different water level. The maximum height difference then depends on the power of the pump (how much work it can do per unit time, or technically how much water it can move back up per unit time). Note that since energy is flowing into the system at one point, the new equilibrium IS unequal water levels (it stays unequal so long as you keep the pump on). If you turned the pump off, the water level equalises quickly.
Same thing for a waterfall. Why is there always water at the top of the waterfall to keep it flowing even though all the water should logically be at the bottom? The sun is providing the energy to evaporate water from the bottom creating clouds and rain to put water back on top--rinse and repeat.
Always look for an energy source--it is the reason for a different equilibrium condition.