In a method and system for controlling base station processing unit overload and buffer overflow in a unified manner, one or more processing units of the base station are monitored to determine if the processing unit(s) has entered an overload condition. If so, on a per flow basis, the system generates an advertise window for controlling the amount of data in the data flow, as transmitted to the processing unit from an upstream entity. The advertise window is generated taking into consideration both processor overload and buffer overflow factors. By incorporating these factors, the advertise windows collectively serve to limit both processor overload and buffer overflow, on a system wide basis.