Generally, energy within a system will tend to distribute until thermodynamic equilibrium is reached. But for a lot of systems that we study, it's a fair assumption that it's coupled to an environment that acts as a large, empty energy sink. So that sink will tend to take all the energy until the system we're interested in ends up in its lowest energy configuration.

For example, an electron orbiting an atom is coupled with the electromagnetic field, which is pretty empty for most situations. So if it's in an excited energy level, it will tend to dump that energy out as a photon until it reaches the ground state. But if the electromagnetic field is locally very active, with photons whizzing around everywhere, this approximation fails and you have to treat the electron's energy level statistically (like in a laser).

Another factor is friction, which in very abstract terms could be defined as the tendency for energy to fall out of macroscopic degrees of freedom towards microscopic. That's what ultimately makes a stirred fluid stop sloshing around, with the energy being dissipated into smaller and smaller vortices until it simply becomes heat.