The tower determines which runway is used at an airport. This is primarily based on the prevailing wind (direction and strength), which can be determined using METAR and TAF. If local specifics are to be considered (e.g. maximum tailwind components for a runway), this can be found in the respective airport SOP.

The tower determines the direction of operation based on where the most traffic is on the Apron.

The approach controller determines which runway is in use depending on the incoming traffic. 

2 VFR arrivals on the same route, follwing aircraft is faster

IFR arrival on final, VFR orbiting abeam the threshold

IFR is cleared for take-off with a VFR aircraft in the departure sector

IFR on final, an IFR departure is holding short of the runway

IFR on final (<4 NM), VFR in in the traffic circuit