We analyse a kinetic cycle of the Ca(2+)-ATPase molecular pump using mesoscopic non-equilibrium thermodynamics. The pump is known to generate heat, and by analysing the operation on the mesoscopic level, we are able to introduce a temperature difference and the corresponding heat flux in the description. Integration over the internal coordinates then results in non-linear flux-force relations describing the operation of the pump on the macroscopic level. Specifically, we obtain an expression for the heat flux associated with the active transport and the coupling of heat effects to the transport of ions and the rate of the ATP-hydrolysis.